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  • 1.
    Aquilante, Francesco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Carlson, Rebecca K.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Delcey, Mickael G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    De Vico, Luca
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen O, Denmark..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ferre, Nicolas
    Univ Aix Marseille, CNRS, Inst Chim Radicalaire, Campus Etoile St Jerome Case 521,Ave Esc, F-13397 Marseille 20, France..
    Frutos, Luis Manuel
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Gagliardi, Laura
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy.;Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Giussani, Angelo
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Hoyer, Chad E.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Li Manni, Giovanni
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Lischka, Hans
    Texas Tech Univ, Dept Chem & Biochem, Mem Circle & Boston, Lubbock, TX 79409 USA.;Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Ma, Dongxia
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Malmqvist, Per Ake
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Mueller, Thomas
    Forschungszentrum Julich, IAS, JSC, Wilhelm Johnen Str, D-52425 Julich, Germany..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, 141 Overman Hall, Bowling Green, OH 43403 USA.;Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam, IL-91904 Jerusalem, Israel..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, POB 1033 Blindern, N-0315 Oslo, Norway..
    Peng, Daoling
    S China Normal Univ, Coll Chem & Environm, Guangzhou 510006, Guangdong, Peoples R China..
    Plasser, Felix
    Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Pritchard, Ben
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Reiher, Markus
    ETH, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Rivalta, Ivan
    Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Schapiro, Igor
    Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France..
    Segarra-Marti, Javier
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Truhlar, Donald G.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Ungur, Liviu
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Valentini, Alessio
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Vancoillie, Steven
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Veryazov, Valera
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Vysotskiy, Victor P.
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Weingart, Oliver
    Univ Dusseldorf, Inst Theoret Chem & Computerchem, Univ Str 1, D-40225 Dusseldorf, Germany..
    Zapata, Felipe
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, p. 506-541Article in journal (Refereed)
    Abstract [en]

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

  • 2. Aquilante, Francesco
    et al.
    De Vito, Luca
    Ferré, Nicolas
    Chigo, Giovanni
    Malmqvist, Per-Åke
    Neogrády, Pavel
    Pedersen, Tjomas Bono
    Pitoňák, Michak
    Reiher, Markus
    Roos, Björn O
    Serrano-Andrés, Luis
    Miroslav, Urban
    Veryazov, Valera
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Software news and update MOLCAS 7: The Next Generation2010In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 31, no 1, p. 224-247Article, review/survey (Refereed)
    Abstract [en]

    Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.

  • 3. Bondesson, Laban
    et al.
    Rudberg, Elias
    Luo, Yi
    Salek, Pawel
    Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, p. 1725-1732Article in journal (Refereed)
  • 4.
    Delcey, Mickael G
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sörensen, Lasse Kragh
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Couto, Rafael Carvalho
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions2019In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, no 19, p. 1789-1799Article in journal (Refereed)
    Abstract [en]

    Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies.

  • 5. Dong, Hua
    et al.
    Chen, Bo-Zhen
    Huang, Ming-Bao
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    The bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 5, p. 537-549Article in journal (Refereed)
    Abstract [en]

    The Bergman cyclizations of the enediyne and its four N-substituted analogs [(Z)-pent-2-en-4-ynenitrile, 3-azahex-3-en-1,5-diyne, malenotrile, and 3,4-azahex-3-en-1,5-diyne] have been studied using the complete active space self-consistent field and multiconfigurational second-order perturbation theory methods in conjunction with the atomic natural orbital basis sets. The geometries and energies of the reactants, transition states, and products along both the S0 (the ground state) and T1 (the lowest-lying triplet state) potential energy surfaces (PESs) were calculated. The calculated geometries are in good agreement with the available experimental data. The distance between two terminal carbons in enediyne, which was considered as an important parameter governing the Bergman cyclization, was predicted to be 4.319 angstrom, in agreement with the experimental value of 4.321 angstrom. Our calculations indicate that the replacements of the terminal C atom(s) or the middle C atom(s) in the C-C bond by the N atom(s) increase or decrease the energy barrier values, respectively. There exist stable ring biradical products on the T1 PESs for the five reactions. However, on the S0 PESs the ring biradical products exist only for the reactions of enediyne, (Z)-pent-2-en-4-ynenitrile, and 3-azahex-3-en-1,5-diyne.

  • 6.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuán, Daniel
    Universitat de València, Spain.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Università di Bologna, Italy.
    A Two-Scale Approach to Electron Correlation in Multiconfigurational Perturbation Theory2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 22, p. 1609-1617Article, review/survey (Refereed)
    Abstract [en]

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

  • 7.
    Hellström, Matti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry. Uppsala Univ, Dept Chem Angstrom, SE-75121 Uppsala, Sweden..
    Treatment of Delocalized Electron Transfer in Periodic and Embedded Cluster DFT Calculations: The Case of Cu on ZnO (10(1)over-bar0)2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 32, p. 2394-2405Article in journal (Refereed)
    Abstract [en]

    We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10 (1) over bar0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10 (1) over bar0), as long as care is taken to account for the effects of CT.

  • 8. Holt, Asbjorn
    et al.
    Boström, Jonas
    Karlström, Gunnar
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    A NEMO potential that includes the dipole-quadrupole and quadrupole-quadrupole polarizability2010In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 31, no 8, p. 1583-1591Article in journal (Refereed)
    Abstract [en]

    To increase the accuracy of molecular force fields a systematical and balanced improvement of the various terms included is needed. In this work, we have followed this strategy to improve the quality of the NEMO potential for the formaldehyde dimer by introducing local quadrupole moments and higher-order polarizabilities. It is found that inclusion of the quadrupole moment significantly improves the interaction potential. Furthermore, the inclusion of higher-order polarizabilities up to quadrupole-quadrupole polarizability is shown to give a better description of the intermolecular interaction. In addition, it is demonstrated that localized properties based on MP2 densities reproduces the BSSE corrected MP2 interaction energy at large intermolecular separations. This is not the case for HF-SCF based properties.

  • 9.
    Jayasinghe-Arachchige, Vindi M.
    et al.
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Hu, Qiaoyu
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Sharma, Gaurav
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Paul, Thomas J.
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Quinonero, David
    Univ Illes Balears, Dept Chem, Palma de Mallorca, Spain.
    Parac-Vogt, Tatjana N.
    Katholieke Univ Leuven, Dept Chem, B-3001 Leuven, Belgium.
    Prabhakar, Rajeev
    Univ Miami, Dept Chem, Coral Gables, FL 33146 USA.
    Hydrolysis of Chemically Distinct Sites of Human Serum Albumin by Polyoxometalate: A Hybrid QM/MM (ONIOM) Study2019In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, no 1, p. 51-61Article in journal (Refereed)
    Abstract [en]

    In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH) (PW11O39)](4-)(ZrK) have been investigated using the hybrid two-layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392-Glu393 site of HSA is predicted to occur in the rate-limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392-Glu393, Ala257-Asp258, Lys313-Asp314, and Arg114-Leu115) for the hydrolysis of all four sites of HSA. (C) 2018 Wiley Periodicals, Inc.

  • 10. Kutzner, Carsten
    et al.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Fechner, Martin
    Lindahl, Erik
    Schmitt, Udo W.
    de Groot, Bert L.
    Grubmüller, Helmut
    Speeding up parallel GROMACS on high-latency networks2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 12, p. 2075-2084Article in journal (Refereed)
    Abstract [en]

    We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clusters with only limited bandwidth and high latency. GROMACS 3.3 scales well on supercomputers like the IBM p690 (Regatta) and on Linux clusters with a special interconnect like Myrinet or Infiniband. Because of the high single-node performance of GROMACS, however, on the widely used Ethernet switched clusters, the scaling typically breaks down when more than two computer nodes are involved, limiting the absolute speedup that can be gained to about 3 relative to a single-CPU run. With the LAM MPI implementation, the main scaling bottleneck is here identified to be the all-to-all communication which is required every time step. During such an all-to-all communication step, a huge amount of messages floods the network, and as a result many TCP packets are lost. We show that Ethernet flow control prevents network congestion and leads to substantial scaling improvements. For 16 CPUs, e.g., a speedup of 11 has been achieved. However, for more nodes this mechanism also fails. Having optimized an all-to-all routine, which sends the data in an ordered fashion, we show that it is possible to completely prevent packet loss for any number of multi-CPU nodes. Thus, the GROMACS scaling dramatically improves, even for switches that lack flow control. In addition, for the common HP ProCurve 2848 switch we find that for optimum all-to-all performance it is essential how the nodes are connected to the switch's ports. This is also demonstrated for the example of the Car-Parinello MD code.

  • 11. Lemkul, Justin A.
    et al.
    Roux, Benoit
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    MacKerell, Alexander D., Jr.
    Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 19, p. 1473-1479Article in journal (Refereed)
    Abstract [en]

    Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nose-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field.

  • 12.
    Lindh, Roland
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Malmquist, PA
    A submatrix algorithm for the matrix-vector multiplication of very large matrices1989In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 10, no 3, p. 344-345Article in journal (Refereed)
    Abstract [en]

    In self-consistent field (SCF) calculations the construction of the Fock matrix is most time-consuming step. The Fock matrix construction may formally be seen as a matrix-vector multiplication, where the matrix is the supermatrix,��ijkl, and the vector is the first-order density matrix, γij. This formalism should be optimal for vector machines. This is not, however, fully utilized in most programs running on computers with small core memory. The size of the �� matrix, typically in the order of 106–108 elements, has forced programmers to implement other nonvectorizable methods. We will present a submatrixbased algorithm which will partition the supermatrix so that vectorizable methods can be employed. The method will also reduce the input/output.

  • 13.
    Lundberg, Marcus
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan..
    Understanding Cross-Boundary Events in ONIOM QM:QM' Calculations2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 4, p. 406-415Article in journal (Refereed)
    Abstract [en]

    QM:QM' models, where QM' is a fast molecular orbital method, offers advantages over standard quantum mechanics: molecular mechanics (QM:MM) models, especially in the description of charge transfer and mutual polarization between layers. The ONIOM QM:QM' scheme also allows for reactions across the layer boundary, but the understanding of these events is limited. To explain the factors that affect cross-boundary events, a set of proton transfer processes, including the acylation reaction in serine protease, have been investigated. For reactions inside out, that is, when a group breaks a bond in the high layer and forms a new bond with a group in the low layer, QM' methods that are overbinding relative to the QM method, for example, Hartree-Fock versus B3LYP, can severely overestimate the exothermicity of the reaction. This might lead to artificial reactivity across the QM:QM' boundary, a phenomenon called model escape. The accuracy for reactions that occur outside in, that is, when a group in the low layer forms a new bond with the high layer, is mainly determined by the QM' calculation. Cross-boundary reactions should generally be avoided in the present ONIOM scheme. Fortunately, a better understanding of these events makes it easy to design stable ONIOM QM:QM' models, for example, by choosing a proper model system. Importantly, an accurate description of cross-boundary reactions would open up possibilities to simulate chemical reactions without a priori limiting the reactivity in the design of the computational model. Challenges to implement a simulation scheme (ONIOM-XR) that can automatically handle chemical reactions between different layers are briefly discussed.

  • 14.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm University, AlbaNova University Center.
    Siegbahn, Per E. M.
    Agreement between experiment and hybrid DFT calculations for O-H bond dissociation enthalpies in manganese complexes2005In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 26, no 7, p. 661-667Article in journal (Refereed)
    Abstract [en]

    Information on the accuracy of DFT functionals for redox reactions in transition metal systems is rather limited. To analyze the performance of some popular functionals for redox reactions in manganese systems, calculated O-H bond dissociation enthalpies for Mn-ligands in six different complexes are compared to experimental results. In this benchmark, B3LYP performs well with a mean absolute error of 3.0 kcal/mol. B98 gives similar results to B3LYP (error of 3.8 kcal/mol). B3LYP* gives lower O-H bond strengths than B3LYP and has a mean error of 5.0 kcal/tnol. Compared to B98 and B3LYP, B3LYP* has an error trend for the manganese ligands that is more similar to the error for a free water molecule. The nonhybrid functional BLYP consistently and significantly underestimates the O-H bond strengths by approximately 20 kcal/mol. HCTH407 has a rather large mean error of 9.4 kcal/mol and shows no consistent trend. The results support the use of hybrid functionals and the present computational method for large model systems containing manganese. An example is the oxygen evolving complex in photosystem 11 where hybrid functionals predict the appearance of a Mn(IV)-oxyl radical before the O-O bond formation step.

  • 15. Lundborg, Magnus
    et al.
    Apostolov, Rossen
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Gardenäs, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Lindahl, Erik
    An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 3, p. 260-269Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present Trajectory Next Generation (TNG)a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes. 

  • 16. Merlot, Patrick
    et al.
    Kjaergaard, Thomas
    Helgaker, Trygve
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Reine, Simen
    Pedersen, Thomas Bondo
    Attractive electron-electron interactions within robust local fitting approximations2013In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 17, p. 1486-1496Article in journal (Refereed)
    Abstract [en]

    An analysis of Dunlap's robust fitting approach reveals that the resulting two-electron integral matrix is not manifestly positive semidefinite when local fitting domains or non-Coulomb fitting metrics are used. We present a highly local approximate method for evaluating four-center two-electron integrals based on the resolution-of-the-identity (RI) approximation and apply it to the construction of the Coulomb and exchange contributions to the Fock matrix. In this pair-atomic resolution-of-the-identity (PARI) approach, atomic-orbital (AO) products are expanded in auxiliary functions centered on the two atoms associated with each product. Numerical tests indicate that in 1% or less of all HartreeFock and KohnSham calculations, the indefinite integral matrix causes nonconvergence in the self-consistent-field iterations. In these cases, the two-electron contribution to the total energy becomes negative, meaning that the electronic interaction is effectively attractive, and the total energy is dramatically lower than that obtained with exact integrals. In the vast majority of our test cases, however, the indefiniteness does not interfere with convergence. The total energy accuracy is comparable to that of the standard Coulomb-metric RI method. The speed-up compared with conventional algorithms is similar to the RI method for Coulomb contributions; exchange contributions are accelerated by a factor of up to eight with a triple-zeta quality basis set. A positive semidefinite integral matrix is recovered within PARI by introducing local auxiliary basis functions spanning the full AO product space, as may be achieved by using Cholesky-decomposition techniques. Local completion, however, slows down the algorithm to a level comparable with or below conventional calculations. 

  • 17. Mishra, Sushil Kumar
    et al.
    Sund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Koca, Jaroslav
    Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 29, p. 2340-2350Article in journal (Refereed)
    Abstract [en]

    The linear interaction energy (LIE) method to compute binding free energies is applied to lectin-monosaccharide complexes. Here, we calculate the binding free energies of monosaccharides to the Ralstonia solanacearum lectin (RSL) and the Pseudomonas aeruginosa lectin-II (PA-IIL). The standard LIE model performs very well for RSL, whereas the PA-IIL system, where ligand binding involves two calcium ions, presents a major challenge. To overcome this, we explore a new variant of the LIE model, where ligandmetal ion interactions are scaled separately. This model also predicts the saccharide binding preference of PA-IIL on mutation of the receptor, which may be useful for protein engineering of lectins.

  • 18. Mueller, Carsten
    et al.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Calculation of the stability of nonperiodic solids using classical force fields and the method of increments: N(2)o as an example2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 18, p. 1420-1427Article in journal (Refereed)
    Abstract [en]

    Combining classical force fields for the Hartree-Fock (HF) part and the method of increments for post-HF contributions, we calculate the cohesive energy of the ordered and randomly disordered nitrous oxide (N2O) solid. At 0 K, ordered N2O is most favorable with a cohesive energy of -27.7 kJ/mol. At temperatures above 60 K, more disordered structures become compatible and a phase transition to completely disordered N2O is predicted. Comparison with experiment in literature suggests that experimentally prepared N2O crystals are mainly disordered due to a prohibitively high activation energy of ordering processes.

  • 19. Nantasenamat, Chanin
    et al.
    Simeon, Saw
    Owasirikul, Wiwat
    Songtawee, Napat
    Lapins, Maris
    Prachayasittikul, Virapong
    Wikberg, Jarl E. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Illuminating the Origins of Spectral Properties of Green Fluorescent Proteins via Proteochemometric and Molecular Modeling2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 27, p. 1951-1966Article in journal (Refereed)
    Abstract [en]

    Green fluorescent protein (GFP) has immense utility in biomedical imaging owing to its autofluorescent nature. In efforts to broaden the spectral diversity of GFP, there have been several reports of engineered mutants via rational design and random mutagenesis. Understanding the origins of spectral properties of GFP could be achieved by means of investigating its structure-activity relationship. The first quantitative structure-property relationship study for modeling the spectral properties, particularly the excitation and emission maximas, of GFP was previously proposed by us some years ago in which quantum chemical descriptors were used for model development. However, such simplified model does not consider possible effects that neighboring amino acids have on the conjugated pi-system of GFP chromophore. This study describes the development of a unified proteochemometric model in which the GFP chromophore and amino acids in its vicinity are both considered in the same model. The predictive performance of the model was verified by internal and external validation as well as gamma-scrambling. Our strategy provides a general solution for elucidating the contribution that specific ligand and protein descriptors have on the investigated spectral property, which may be useful in engineering novel GFP variants with desired characteristics.

  • 20.
    Norberg, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Salhi-Benachenhou, Nessima
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal: A theoretical investigation of the concerted and stepwise mechanisms2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 3, p. 392-406Article in journal (Refereed)
    Abstract [en]

    The stepwise and concerted pathways for the McLafferty rearrangement of the radical cations of butanal (Bu+) and 3-fluorobutanal (3F-Bu+) are investigated with density functional theory (DFT) and ab initio methods in conjunction with the 6-311+G(d,p) basis set. A concerted transition structure (TS) for Bu+ (H), is located with a Gibbs barrier height of 37.7 kcal/mol as computed with CCSD(T)//BHandHLYP. Three pathways for the stepwise rearrangement of Bu+ have been located, which are all found to involve different complexes. The barrier height for the H, transfer is found to be 2.2 kcal/mol, while the two most favorable TSs for the C-alpha-C-beta cleavage are located 8.9 and 9.2 kcal/mol higher. The energies of the 3F-Bu+ system have been calculated with the promising hybrid meta-GGA MPWKCIS1K functional of DFT. Interestingly, the fluorine substitution yields a barrier height of only 20.5 kcal/mol for the concerted TS, (3F-H). A smaller computed dipole moment, 12.1 D, for (3F-H) compared with 103.2 D for (H) might explain the stabilization of the substituted TS. The H. transfer, with a barrier height of 4.9 kcal/mol, is found to be rate-determining for the stepwise McLafferty rearrangement of 3F-Bu+, in contrast to the unsubstituted case. By inspection of the spin and charge distributions of the stationary points, it is noted that the bond cleavages in the concerted rearrangements are mainly of heterolytic nature, while those in the stepwise channels are found to be homolytic.

  • 21.
    Orthaber, Andreas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Sax, Alexander F.
    Francesconi, Kevin A.
    Oxygen Versus Sulfur: Structure and Reactivity of Substituted Arsine Oxides and Arsine Sulfides2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 1, p. 112-117Article in journal (Refereed)
    Abstract [en]

    Although arsenic in its inorganic forms is a well know toxic agent, biotransformations in the environment and in the human body can produce organoarsenic compounds that are generally of much lower toxicity. Foremost among these products is a range of dimethylated arsine oxides and their analogous sulfides, which are crucial to the arsenic detoxification process. We have investigated the formation and interconversion of substituted and unsubstituted arsenicals (R(2)(2)As(=Z)R(1), R(2) = CH(3), R(1) = CH(2)CH(2)OH, CH(2)COOH; Z = S or O) with density functional theory (DFT)/B3LYP. Formation of isomers including a cyclic hydrogen bonded conformer is observed for the ethanol and acetate derivatives. Furthermore, investigating the reaction of arsine oxide with hydrogen sulfide revealed the formation of arsine sulfide via pentacoordinated trigonal bipyramidal intermediates. A tetragonal pyramidal transition state was located enabling exchange of equatorial and axial positions in the trigonal bipyramidal species. The reaction was proven exothermic for all studied substituents (Delta E(rxn) -50 to -80 kJ/mol). This fundamental study shows that H(2)S easily leads to the formation of thioorganoarsenicals. Conversion of arsine sulfides into their corresponding arsine oxides is experimentally accomplished with hydrogen peroxide, which could also be rationalized by means of ab initio calculations showing high exothermicity (Delta E(rxn) ca. -550 kJ/mol). Reactions are considered at different levels of theory (i.e., DFT, second and fourth order Moller-Plesset (MP) perturbation theory) including two solvation models for DFT, which show good agreement for resulting geometries and reaction energies. Hence, the widely used B3LYP/6-31G** combination is a suitable method for the description of molecular organoarsenicals.

  • 22. Pinjari, Rahul V.
    et al.
    Delcey, Mickaël G
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Odelius, Michael
    Lundberg, Marcus
    Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987XArticle in journal (Refereed)
  • 23.
    Pinjari, Rahul V.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Swami Ramanand Teerth Marathwada Univ, Sch Chem Sci, Nanded 431606, Maharashtra, India.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, p. 477-486Article in journal (Refereed)
    Abstract [en]

    The restricted active-space (RAS) approach can accurately simulate metal L-edge X-ray absorption spectra of first-row transition metal complexes without the use of any fitting parameters. These characteristics provide a unique capability to identify unknown chemical species and to analyze their electronic structure. To find the best balance between cost and accuracy, the sensitivity of the simulated spectra with respect to the method variables has been tested for two models, [FeCl6](3-) and [Fe(CN)(6)](3-). For these systems, the reference calculations give deviations, when compared with experiment, of 1 eV in peak positions, 30% for the relative intensity of major peaks, and 50% for minor peaks. When compared with these deviations, the simulated spectra are sensitive to the number of final states, the inclusion of dynamical correlation, and the ionization potential electron affinity shift, in addition to the selection of the active space. The spectra are less sensitive to the quality of the basis set and even a double- basis gives reasonable results. The inclusion of dynamical correlation through second-order perturbation theory can be done efficiently using the state-specific formalism without correlating the core orbitals. Although these observations are not directly transferable to other systems, they can, together with a cost analysis, aid in the design of RAS models and help to extend the use of this powerful approach to a wider range of transition metal systems.

  • 24.
    Roca-Sanjuan, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Mazziotti, D. A.
    Univ Chicago, James Franck Inst, Dept Chem, Chicago, IL 60637 USA.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Comment on "€œDensity functional theory study of 1,2-€dioxetanone decomposition in condensed phase€"2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 26, p. 2124-2126Article in journal (Refereed)
    Abstract [en]

    In the preceding paper results are presented, which are in serious conflict with state-of-the-art ab initio method. Based on these new results the authors propose a new explanation of the reason for the preferential production of a phosphorescent state. Here we show that these controversial results are flawed, since the model use exclude biradical electron structures.

  • 25.
    Rubensson, Emanuel H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Bringing about matrix sparsity in linear-scaling electronic structure calculations2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, p. 1411-1423Article in journal (Refereed)
  • 26. Rubensson, Emanuel H.
    et al.
    Rudberg, Elias
    Salek, Pawel
    A hierarchic sparse matrix data structure for large-scale Hartree-Fock/Kohn-Sham calculations2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 16, p. 2531-2537Article in journal (Refereed)
  • 27. Rubensson, Emanuel H.
    et al.
    Rudberg, Elias
    Salek, Pawel
    Truncation of Small Matrix Elements Based on the Euclidean Norm for Blocked Data Structures2009In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 30, no 6, p. 974-977Article in journal (Refereed)
  • 28. Rubensson, Emanuel H.
    et al.
    Salek, Pawel
    Systematic sparse matrix error control for linear scaling electronic structure calculations2005In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 26, no 15, p. 1628-1637Article in journal (Refereed)
  • 29.
    Sanchez, M. Luz
    et al.
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Corchado, Jose C.
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Martin, M. Elena
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Fdez. Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Barata-Morgado, Rute
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Aguilar, Manuel A.
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    A new QM/MM method oriented to the study of ionic liquids2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 25, p. 1893-1901Article in journal (Refereed)
    Abstract [en]

    The interest on room temperature ionic liquids has grown in the last decades because of their use as all-purpose solvent and their low environmental impact. In the present work, a new theoretical procedure is developed to study pure ionic liquids within the framework of the quantum mechanics/molecular mechanics method. Each type of ion (cation or anion) is considered as an independent entity quantum mechanically described that follows a differentiated path in the liquid. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1-ethyl-3-methylimidazolium tetrafluoroborate. It was found that, similar to non-polar liquids and as a consequence of the low value of the reaction field, the cation and anion charge distributions are hardly polarized by the rest of molecules in the liquid. Their structure is characterized by an alternance between anion and cation shells as evidenced by the coincidence of the first maximum of the anion-anion and cation-cation radial distribution functions with the first minimum of the anion-cation. Some degree of stacking between the cations is also found.

  • 30. Schapiro, Igor
    et al.
    Roca-Sanjuán, Daniel
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Olivucci, Massimo
    A surface hopping algorithm for nonadiabatic minimum energy path calculations2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 5, p. 312-20Article in journal (Refereed)
    Abstract [en]

    The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base.

  • 31.
    Sieradzan, Adam K.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
    Introduction of Periodic Boundary Conditions into UNRES Force Field2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 12, p. 940-946Article in journal (Refereed)
    Abstract [en]

    In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the hetero tetramer 1 protein system.

  • 32.
    Stenrup, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Galvan, Ignacio Fdez.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Constrained numerical gradients and composite gradients: Practical tools for geometry optimization and potential energy surface navigation2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 22, p. 1698-1708Article in journal (Refereed)
    Abstract [en]

    A method is proposed to easily reduce the number of energy evaluations required to compute numerical gradients when constraints are imposed on the system, especially in connection with rigid fragment optimization. The method is based on the separation of the coordinate space into a constrained and an unconstrained space, and the numerical differentiation is done exclusively in the unconstrained space. The decrease in the number of energy calculations can be very important if the system is significantly constrained. The performance of the method is tested on systems that can be considered as composed of several rigid groups or molecules, and the results show that the error with respect to conventional optimizations is of the order of the convergence criteria. Comparison with another method designed for rigid fragment optimization proves the present method to be competitive. The proposed method can also be applied to combine numerical and analytical gradients computed at different theory levels, allowing an unconstrained optimization with numerical differentiation restricted to the most significant degrees of freedom. This approach can be a practical alternative when analytical gradients are not available at the desired computational level and full numerical differentiation is not affordable. (c) 2015 Wiley Periodicals, Inc.

  • 33. Söderhjelm, P.
    et al.
    Krogh, J W
    Karlström, G
    Ryde, U
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 6, p. 1083-1090Article in journal (Refereed)
    Abstract [en]

    Localized multipole moments up to the fifth moment as well as localized dipole polarizabilities are calculated with the MpProp and the newly developed LoProp methods for a total of 20 molecules, predominantly derived from amino acids. A comparison of electrostatic potentials calculated from the multipole expansion obtained by the two methods with ab initio results shows that both methods reproduce the electrostatic interaction with an elementary charge with a mean absolute error of similar to 1.5 kJ/mol at contact distance and less than 0.1 kJ/mol at distances 2 angstrom further out when terms up to the octupole moments are included. The polarizabilities are tested with homogenous electric fields and are-found to have similar accuracy. The MpProp method gives better multipole moments unless diffuse basis sets are used, whereas LoProp gives better polarizabilities.

  • 34. Vancoillie, Steven
    et al.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Vysotskiy, Victor
    Malmqvist, Per-Ake
    Veryazov, Valera
    Parallelization of a multiconfigurational perturbation theory2013In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 22, p. 1937-1948Article in journal (Refereed)
    Abstract [en]

    In this work, we present a parallel approach to complete and restricted active space second-order perturbation theory, (CASPT2/RASPT2). We also make an assessment of the performance characteristics of its particular implementation in the Molcas quantum chemistry programming package. Parallel scaling is limited by memory and I/O bandwidth instead of available cores. Significant time savings for calculations on large and complex systems can be achieved by increasing the number of processes on a single machine, as long as memory bandwidth allows, or by using multiple nodes with a fast, low-latency interconnect. We found that parallel efficiency drops below 50% when using 8-16 cores on the shared-memory architecture, or 16-32 nodes on the distributed-memory architecture, depending on the calculation. This limits the scalability of the implementation to a moderate amount of processes. Nonetheless, calculations that took more than 3 days on a serial machine could be performed in less than 5 h on an InfiniBand cluster, where the individual nodes were not even capable of running the calculation because of memory and I/O requirements. This ensures the continuing study of larger molecular systems by means of CASPT2/RASPT2 through the use of the aggregated computational resources offered by distributed computing systems.

1 - 34 of 34
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