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

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

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

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

  • 3.
    Ammothum Kandy, Akshay Krishna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Wadbro, Eddie
    Aradi, Bálint
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Curvature Constrained Splines for DFTB Repulsive Potential Parametrization2021In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 17, no 3, p. 1771-1781Article in journal (Refereed)
    Abstract [en]

    The Curvature Constrained Splines (CCS) methodology has been used for fitting repulsive potentials to be used in SCC-DFTB calculations. The benefit of using CCS is that the actual fitting of the repulsive potential is performed through quadratic programming on a convex objective function. This guarantees a unique (for strictly convex) and optimum two-body repulsive potential in a single shot, thereby making the parametrization process robust, and with minimal human effort. Furthermore, the constraints in CCS give the user control to tune the shape of the repulsive potential based on prior knowledge about the system in question. Herein, we developed the method further with new constraints and the capability to handle sparse data. We used the method to generate accurate repulsive potentials for bulk Si polymorphs and demonstrate that for a given Slater-Koster table, which reproduces the experimental band structure for bulk Si in its ground state, we are unable to find one single two-body repulsive potential that can accurately describe the various bulk polymorphs of silicon in our training set. We further demonstrate that to increase transferability, the repulsive potential needs to be adjusted to account for changes in the chemical environment, here expressed in the form of a coordination number. By training a near-sighted Atomistic Neural Network potential, which includes many-body effects but still essentially within the first-neighbor shell, we can obtain full transferability for SCC-DFTB in terms of describing the energetics of different Si polymorphs.

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

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

  • 5.
    Battaglia, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Fransén, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Regularized CASPT2: an Intruder-State-Free Approach2022In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 8, p. 4814-4825Article in journal (Refereed)
    Abstract [en]

    In this work we present a new approach to fix the intruder-state problem (ISP) in CASPT2 based on sigma p regularization. The resulting sigma(p)-CASPT2 method is compared to previous techniques, namely, the real and imaginary level shifts, on a theoretical basis and by performing a series of systematic calculations. The analysis is focused on two aspects, the effectiveness of sigma(p)-CASPT2 in removing the ISP and the sensitivity of the approach with respect to the input parameter. We found that sigma p- CASPT2 compares favorably with respect to previous approaches and that different versions, sigma(1)-CASPT2 and sigma(2)-CASPT2, have different potential application domains. This analysis also reveals the unsuitability of the real level shift technique as a general way to avoid the intruder-state problem.

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  • 6.
    Battaglia, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Extended Dynamically Weighted CASPT2: The Best of Two Worlds2020In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 16, no 3, p. 1555-1567Article in journal (Refereed)
    Abstract [en]

    We introduce a new variant of the complete active A space second-order perturbation theory (CASPT2) method that performs similarly to multistate CASPT2 (MS-CASPT2) in regions of the potential energy surface where the electronic states are energetically well separated and is akin to extended MS-CASPT2 (XMS-CASPT2) in case the underlying zeroth-order references are near-degenerate. Our approach follows a recipe analogous to that of XMS-CASPT2 to ensure approximate invariance under unitary transformations of the model states and a dynamic weighting scheme to smoothly interpolate the Fock operator between state-specific and state-average regimes. The resulting extended dynamically weighted CASPT2 (XDW-CASPT2) methodology possesses the most desirable features of both MS-CASPT2 and XMS-CASPT2, that is, the ability to provide accurate transition energies and correctly describe avoided crossings and conical intersections. The reliability of XDW-CASPT2 is assessed on a number of molecular systems. First, we consider the dissociation of lithium fluoride, highlighting the distinctive characteristics of the new approach. Second, the invariance of the theory is investigated by studying the conical intersection of the distorted allene molecule. Finally, the relative accuracy in the calculation of vertical excitation energies is benchmarked on a set of 26 organic compounds. We found that XDW-CASPT2, albeit being only approximately invariant, produces smooth potential energy surfaces around conical intersections and avoided crossings, performing equally well to the strictly invariant XMS-CASPT2 method. The accuracy of vertical transition energies is almost identical to MS-CASPT2, with a mean absolute deviation of 0.01-0.02 eV, in contrast to 0.12 eV for XMS-CASPT2.

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

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

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

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

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

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

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

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

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

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

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

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

  • 13.
    Brumboiu, Iulia Emilia
    et al.
    KTH Royal Inst Technol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden;Korea Adv Inst Sci & Technol, Dept Chem, Daejeon 34141, South Korea.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Orebro Univ, Sch Sci & Technol, S-70182 Orebro, Sweden.
    Norman, Patrick
    KTH Royal Inst Technol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden.
    Photoelectron Spectroscopy of Molecules Beyond the Electric Dipole Approximation2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 10, p. 5483-5494Article in journal (Refereed)
    Abstract [en]

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

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    FULLTEXT01
  • 14. Caleman, Carl
    et al.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hong, Minyan
    Hub, Jochen S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Costa, Luciano T.
    van der Spoer, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 1, p. 61-74Article in journal (Refereed)
    Abstract [en]

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

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

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

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

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

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

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

  • 18. Cuéllar-Zuquin, Juliana
    et al.
    Pepino, Ana Julieta
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Rivalta, Ivan
    Aquilante, Francesco
    Garavelli, Marco
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Segarra-Martí, Javier
    Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 22, p. 8258-8272Article in journal (Refereed)
    Abstract [en]

    We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.

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

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

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

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

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

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

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

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

  • 23.
    Dufils, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Knijff, Lisanne
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Shao, Yunqi
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Zhang, Chao
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    PiNNwall: Heterogeneous Electrode Models from Integrating Machine Learning and Atomistic Simulation2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 15, p. 5199-5209Article in journal (Refereed)
    Abstract [en]

    Electrochemical energy storage always involves the capacitive process. The prevailing electrode model used in the molecular simulation of polarizable electrode–electrolyte systems is the Siepmann–Sprik model developed for perfect metal electrodes. This model has been recently extended to study the metallicity in the electrode by including the Thomas–Fermi screening length. Nevertheless, a further extension to heterogeneous electrode models requires introducing chemical specificity, which does not have any analytical recipes. Here, we address this challenge by integrating the atomistic machine learning code (PiNN) for generating the base charge and response kernel and the classical molecular dynamics code (MetalWalls) dedicated to the modeling of electrochemical systems, and this leads to the development of the PiNNwall interface. Apart from the cases of chemically doped graphene and graphene oxide electrodes as shown in this study, the PiNNwall interface also allows us to probe polarized oxide surfaces in which both the proton charge and the electronic charge can coexist. Therefore, this work opens the door for modeling heterogeneous and complex electrode materials often found in energy storage systems.

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  • 24.
    Elias-Wolff, Federico
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden; Stockholm Univ, Dept Mat & Environm Chem, Stockholm, Sweden.
    Lindén, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Lyubartsev, Alexander P.
    Stockholm Univ, Dept Mat & Environm Chem, Stockholm, Sweden.
    Brandt, Erik G.
    Stockholm Univ, Dept Mat & Environm Chem, Stockholm, Sweden.
    Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 3, p. 1643-1655Article in journal (Refereed)
    Abstract [en]

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

  • 25.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Revisiting the Nonadiabatic Process in 1,2-Dioxetane2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 12, p. 5404-5411Article in journal (Refereed)
    Abstract [en]

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

  • 26.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Delcey, Mickael G.
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Chem, Kenneth S Pitzer Ctr Theoret Chem, Berkeley, CA 94720 USA..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, POB 1033 Blindern, N-0315 Oslo, Norway..
    Aquilante, Francesco
    Univ Bologna, Dipartimento Chim G Ciamician, Via F Selmi 2, IT-40126 Bologna, Italy..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical State-Average Complete-Active-Space Self-Consistent Field Nonadiabatic Coupling Vectors: Implementation with Density-Fitted Two-Electron Integrals and Application to Conical Intersections2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 8, p. 3636-3653Article in journal (Refereed)
    Abstract [en]

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

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  • 27.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Smooth Things Come in Threes: A Diabatic Surrogate Model for Conical Intersection Optimization2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 11, p. 3418-3427Article in journal (Refereed)
    Abstract [en]

    The optimization of conical intersection structures iscomplicatedby the nondifferentiability of the adiabatic potential energy surfaces.In this work, we build a pseudodiabatic surrogate model, based onGaussian process regression, formed by three smooth and differentiablesurfaces that can adequately reproduce the adiabatic surfaces. Usingthis model with the restricted variance optimization method resultsin a notable decrease of the overall computational effort requiredto obtain minimum energy crossing points.

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  • 28.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Raggi, Gerardo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Restricted-Variance Constrained, Reaction Path, and Transition State Molecular Optimizations Using Gradient-Enhanced Kriging2021In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 17, no 1, p. 571-582Article in journal (Refereed)
    Abstract [en]

    Gaussian process regression has recently been explored as an alternative to standard surrogate models in molecular equilibrium geometry optimization. In particular, the gradient-enhanced Kriging approach in association with internal coordinates, restricted-variance optimization, and an efficient and fast estimate of hyperparameters has demonstrated performance on par or better than standard methods. In this report, we extend the approach to constrained optimizations and transition states and benchmark it for a set of reactions. We compare the performance of the newly developed method with the standard techniques in the location of transition states and in constrained optimizations, both isolated and in the context of reaction path computation. The results show that the method outperforms the current standard in efficiency as well as in robustness.

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  • 29.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Alavi, Ali
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Angeli, Celestino
    Univ Ferrara, Dipartimento Sci Chim & Farmaceut, Via Luigi Borsari 46, I-44121 Ferrara, Italy.
    Aquilante, Francesco
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Bao, Jie J.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Bokarev, Sergey I.
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Bogdanov, Nikolay A.
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Carlson, Rebecca K.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Chibotaru, Liviu F.
    Univ Leuven, Theory Nanomat Grp, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Creutzberg, Joel
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden;Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Dattani, Nike
    Harvard Smithsonian Ctr Astrophys, 60 Garden St, Cambridge, MA 02138 USA.
    Delcey, Mickael G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Dong, Sijia S.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Dreuw, Andreas
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany.
    Freitag, Leon
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Manuel Frutos, Luis
    Univ Alcala De Henares, Dept Quim Analit Quim Fis & Ingn Quim, E-28871 Madrid, Spain;Univ Alcala De Henares, Inst Invest Quim Andres M del Rio, E-28871 Madrid, Spain.
    Gagliardi, Laura
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Gendron, Frederic
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Giussani, Angelo
    UCL, Dept Chem, 20 Gordon St, London WC1H 0AJ, England;Univ Valencia, Inst Ciencia Mol, Apartado 22085, ES-46071 Valencia, Spain.
    Gonzalez, Leticia
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Grell, Gilbert
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Hoyer, Chad E.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Johansson, Marcus
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Keller, Sebastian
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Knecht, Stefan
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Kovacevic, Goran
    Rudjer Boskovic Inst, Div Mat Phys, POB 180,Bijenicka 54, HR-10002 Zagreb, Croatia.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Li Manni, Giovanni
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ma, Yingjin
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Mai, Sebastian
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Malhado, Joao Pedro
    Imperial Coll London, Dept Chem, London SW7 2AZ, England.
    Malmqvist, Per Ake
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Marquetand, Philipp
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Mewes, Stefanie A.
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany;Massey Univ Albany, Ctr Theoret Chem & Phys, NZLAS, Private Bag 102904, Auckland 0632, New Zealand.
    Norell, Jesper
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden.
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via A Moro 2, I-53100 Siena, Italy;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA;Univ Strasbourg, CNRS, USIAS, F-67034 Strasbourg, France;Univ Strasbourg, CNRS, Inst Phys & Chim Mat Strasbourg, F-67034 Strasbourg, France.
    Oppel, Markus
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Phung, Quan Manh
    Pierloot, Kristine
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Plasser, Felix
    Loughborough Univ, Dept Chem, Loughborough LE11 3TU, Leics, England.
    Reiher, Markus
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sand, Andrew M.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, Jerusalem, Israel.
    Sharma, Prachi
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Stein, Christopher J.
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sörensen, Lasse Kragh
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Truhlar, Donald G.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Ugandi, Mihkel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, Singapore 117543, Singapore.
    Valentini, Alessio
    Res Unit MolSys, Theoret Phys Chem, Allee 6 Aout 11, B-4000 Liege, Belgium.
    Vancoillie, Steven
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Weser, Oskar
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Wesolowski, Tomasz A.
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Widmark, Per-Olof
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Wouters, Sebastian
    Brantsandpatents, Pauline van Pottelsberghelaan 24, B-9051 Sint Denijs Westrem, Belgium.
    Zech, Alexander
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Zobel, J. Patrick
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Uppsala Center for Computational Chemistry (UC3), Uppsala University, P.O. Box 596, SE-751 24 Uppsala, Sweden.
    OpenMolcas: From Source Code to Insight2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 11, p. 5925-5964Article in journal (Refereed)
    Abstract [en]

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

  • 30.
    Finkelstein, Joshua
    et al.
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 United States.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Mniszewski, Susan M.
    Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.
    Negre, Christian F. A.
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 United States.
    Niklasson, Anders M. N.
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 United States.
    Quantum Perturbation Theory Using Tensor Cores and a Deep Neural Network2022In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 7, p. 4255-4268Article in journal (Refereed)
    Abstract [en]

    Time-independent quantum response calculations are performed using Tensor cores. This is achieved by mapping density matrix perturbation theory onto the computational structure of a deep neural network. The main computational cost of each deep layer is dominated by tensor contractions, i.e., dense matrix–matrix multiplications, in mixed-precision arithmetics, which achieves close to peak performance. Quantum response calculations are demonstrated and analyzed using self-consistent charge density-functional tight-binding theory as well as coupled-perturbed Hartree–Fock theory. For linear response calculations, a novel parameter-free convergence criterion is presented that is well-suited for numerically noisy low-precision floating point operations and we demonstrate a peak performance of almost 200 Tflops using the Tensor cores of two Nvidia A100 GPUs.

  • 31. Finkelstein, Joshua
    et al.
    Smith, Justin S.
    Mniszewski, Susan M.
    Barros, Kipton
    Negre, Christian F. A.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Niklasson, Anders M. N.
    Mixed Precision Fermi-Operator Expansion on Tensor Cores from a Machine Learning Perspective2021In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 17, no 4, p. 2256-2265Article in journal (Refereed)
    Abstract [en]

    We present a second-order recursive Fermi-operator expansion scheme using mixed precision floating point operations to perform electronic structure calculations using tensor core units. A performance of over 100 teraFLOPs is achieved for half-precision floating point operations on Nvidia’s A100 tensor core units. The second-order recursive Fermi-operator scheme is formulated in terms of a generalized, differentiable deep neural network structure, which solves the quantum mechanical electronic structure problem. We demonstrate how this network can be accelerated by optimizing the weight and bias values to substantially reduce the number of layers required for convergence. We also show how this machine learning approach can be used to optimize the coefficients of the recursive Fermi-operator expansion to accurately represent the fractional occupation numbers of the electronic states at finite temperatures.

  • 32.
    Finkelstein, Joshua
    et al.
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States.
    Smith, Justin S.
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States.
    Mniszewski, Susan M.
    Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States.
    Barros, Kipton
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States.
    Negre, Christian F. A.
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. 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, Numerical Analysis.
    Niklasson, Anders M. N.
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States.
    Quantum-Based Molecular Dynamics Simulations Using Tensor Cores2021In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 17, no 10, p. 6180-6192Article in journal (Refereed)
    Abstract [en]

    Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary computational speed and energy efficiency but with the caveat that they were designed for tensor contractions (matrix-matrix multiplications) using only low-precision floating-point operations. Despite this perceived limitation, we demonstrate how tensor cores can be applied with high efficiency to the challenging and numerically sensitive problem of quantum-based Born-Oppenheimer molecular dynamics, which requires highly accurate electronic structure optimizations and conservative force evaluations. The interatomic forces are calculated on-the-fly from an electronic structure that is obtained from a generalized deep neural network, where the computational structure naturally takes advantage of the exceptional processing power of the tensor cores and allows for high performance in excess of 100 Tflops on a single Nvidia A100 GPU. Stable molecular dynamics trajectories are generated using the framework of extended Lagrangian Born-Oppenheimer molecular dynamics, which combines computational efficiency with long-term stability, even when using approximate charge relaxations and force evaluations that are limited in accuracy by the numerically noisy conditions caused by the low-precision tensor core floating-point operations. A canonical ensemble simulation scheme is also presented, where the additional numerical noise in the calculated forces is absorbed into a Langevin-like dynamics.

  • 33.
    Fischer, Nina M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ditz, Jonas C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Yildirim, Ahmet
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 7, p. 2938-2944Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 35.
    Garcia-Prieto, Francisco F.
    et al.
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Muñoz-Losa, Aurora
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Fdez. Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sanchez, M. Luz
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Aguilar, Manuel A.
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Martin, M. Elena
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 2, p. 737-748Article in journal (Refereed)
    Abstract [en]

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

  • 36.
    Ghahremanpour, Mohammad Mehdi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Hutchison, Geoffrey R.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 11, p. 5553-5566Article in journal (Refereed)
    Abstract [en]

    Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1s-Gaussian or a ns-Slater (n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library (https://doi.org/10.5281/zenodo.1004711) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

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

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

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

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

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

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

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

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

  • 41.
    Grime, John M. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Khan, Malek O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Effects of discrete charge clustering in simulations of charged interfaces2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 10, p. 3205-3211Article in journal (Refereed)
    Abstract [en]

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

  • 42.
    Guo, Meiyuan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Southwest Univ, Dept Chem & Chem Engn, Chongqing, Peoples R China.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pinjari, Rahul V.
    Swami Ramanand Teerth Marathwada Univ, Sch Chem Sci, Nanded, Maharashtra, India.
    Couto, Rafael Carvalho
    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.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pierloot, Kristine
    Univ Leuven, Dept Chem, Heverlee, Belgium.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Siena, Dept Biotechnol Chem & Pharm, Siena, Italy.
    Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 1, p. 477-489Article in journal (Refereed)
    Abstract [en]

    The capability of the multiconfigurational restricted active space approach to identify electronic structure from spectral fingerprints is explored by applying it to iron L-edge X-ray absorption spectroscopy (XAS) of three heme systems that represent the limiting descriptions of iron in the Fe-O-2 bond, ferrous and ferric [Fe(P)(ImH)(2)](0/1+) (P = porphine, ImH = imidazole), and Fe-II(P). The level of agreement between experimental and simulated spectral shapes is calculated using the cosine similarity, which gives a quantitative and unbiased assignment. Further dimensions in fingerprinting are obtained from the L-edge branching ratio, the integrated absorption intensity, and the edge position. The results show how accurate ab initio simulations of metal L-edge XAS can complement calculations of relative energies to identify unknown species in chemical reactions.

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  • 43.
    Gupta, Verena Kristin
    et al.
    Univ Bremen, Bremen Ctr Computat Mat Sci, D-28334 Bremen, Germany..
    Aradi, Balint
    Univ Bremen, Bremen Ctr Computat Mat Sci, D-28334 Bremen, Germany..
    Kweon, Kyoung
    Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94550 USA..
    Keilbart, Nathan
    Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94550 USA..
    Goldman, Nir
    Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94550 USA.;Univ Calif Davis, Dept Chem Engn, Davis, CA 95616 USA..
    Frauenheim, Thomas
    Univ Bremen, Bremen Ctr Computat Mat Sci, D-28334 Bremen, Germany.;Computat Sci Res Ctr, Beijing 100193, Peoples R China.;Computat Sci & Appl Res Inst, Shenzhen 75120, Peoples R China..
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Using DFTB to Model Photocatalytic Anatase-Rutile TiO2 Nanocrystalline Interfaces and Their Band Alignment2021In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 17, no 8, p. 5239-5247Article in journal (Refereed)
    Abstract [en]

    Band alignment effects of anatase and rutile nanocrystals in TiO2 powders lead to electron-hole separation, increasing the photocatalytic efficiency of these powders. While size effects and types of possible alignments have been extensively studied, the effect of interface geometries of bonded nanocrystal structures on the alignment is poorly understood. To allow conclusive studies of a vast variety of bonded systems in different orientations, we have developed a new density functional tight-binding parameter set to properly describe quantum confinement in nanocrystals. By applying this set, we found a quantitative influence of the interface structure on the band alignment.

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  • 44.
    Gustafsson, Hannes
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Kozdra, Melania
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Smit, Berend
    Ecole Polytech Fed Lausanne EPFL, Inst Sci & Ingn Chim, CH-1951 Sion, Switzerland..
    Barthel, Senja
    Vrije Univ, Dept Math, NL-1081 HV Amsterdam, Netherlands..
    Mace, Amber
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Predicting Ion Diffusion from the Shape of Potential Energy Landscapes2024In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 1, p. 18-29Article in journal (Refereed)
    Abstract [en]

    We present an efficient method to compute diffusion coefficients of multiparticle systems with strong interactions directly from the geometry and topology of the potential energy field of the migrating particles. The approach is tested on Li-ion diffusion in crystalline inorganic solids, predicting Li-ion diffusion coefficients within 1 order of magnitude of molecular dynamics simulations at the same level of theory while being several orders of magnitude faster. The speed and transferability of our workflow make it well-suited for extensive and efficient screening studies of crystalline solid-state ion conductor candidates and promise to serve as a platform for diffusion prediction even up to the density functional level of theory.

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  • 45.
    Hellström, Matti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Band-Filling Correction Method for Accurate Adsorption Energy Calculations: A Cu/ZnO Case Study2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 11, p. 4673-4678Article in journal (Refereed)
    Abstract [en]

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

  • 46.
    Henschel, Henning
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Alfred T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jespers, Willem
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ghahremanpour, Mohammad Mehdi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA..
    Van der Spoel, David
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields2020In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 16, no 5, p. 3307-3315Article in journal (Refereed)
    Abstract [en]

    Infrared spectroscopy can provide significant insight into the structures and dynamics of molecules of all sizes. The information that is contained in the spectrum is, however, often not easily extracted without the aid of theoretical calculations or simulations. We present here the calculation of the infrared spectra of a database of 703 gas phase compounds with four different force fields (CGenFF, GAFF-BCC, GAFF-ESP, and OPLS) using normal-mode analysis. Modern force fields increasingly use virtual sites to describe, e.g., lone-pair electrons or the o -holes on halogen atoms. This requires some adaptation of code to perform normal-mode analysis of such compounds, the implementation of which into the GROMACS software is briefly described as well. For the quantitative comparison of the obtained spectra with experimental reference data, we discuss the application of two different statistical correlation coefficients, Pearson and Spearman. The advantages and drawbacks of the different methods of comparison are discussed, and we find that both methods of comparison give the same overall picture, showing that present force field methods cannot match the performance of quantum chemical methods for the calculation of infrared spectra.

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

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

  • 48.
    Hub, Jochen S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    de Groot, Bert L.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 12, p. 3713-3720Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 50.
    Jeong, WooSeok
    et al.
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Stoneburner, Samuel J.
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    King, Daniel
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Li, Ruye
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Walker, Andrew
    Univ Minnesota, Dept Comp Sci & Engn, Minneapolis, MN 55455 USA..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Uppsala Univ, Uppsala Center for Computational Chemistry, S-75123 Uppsala, Sweden..
    Gagliardi, Laura
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Automation of Active Space Selection for Multireference Methods via Machine Learning on Chemical Bond Dissociation2020In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 16, no 4, p. 2389-2399Article in journal (Refereed)
    Abstract [en]

    Predicting and understanding the chemical bond is one of the major challenges of computational quantum chemistry. Kohn-Sham density functional theory (KS-DFT) is the most common method, but approximate density functionals may not be able to describe systems where multiple electronic configurations are equally important. Multiconfigurational wave functions, on the other hand, can provide a detailed understanding of the electronic structures and chemical bonds of such systems. In the complete active space self-consistent field (CASSCF) method, one performs a full configuration interaction calculation in an active space consisting of active electrons and active orbitals. However, CASSCF and its variants require the selection of these active spaces. This choice is not black box; it requires significant experience and testing by the user, and thus active space methods are not considered particularly user-friendly and are employed only by a minority of quantum chemists. Our goal is to popularize these methods by making it easier to make good active space choices. We present a machine learning protocol that performs an automated selection of active spaces for chemical bond dissociation calculations of main group diatomic molecules. The protocol shows high prediction performance for a given target system as long as a properly correlated system is chosen for training. Good active spaces are correctly predicted with a considerably better success rate than random guess (larger than 80% precision for most systems studied). Our automated machine learning protocol shows that a "black-box" mode is possible for facilitating and accelerating the large-scale calculations on multireference systems where single-reference methods such as KS-DFT cannot be applied.

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