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  • 1. Ajitha, D
    et al.
    Wierzbowska, M
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Malmqvist, P A
    Spin-orbit ab initio study of alkyl halide dissociation via electronic curve crossing2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 12, p. 5761-5766Article in journal (Refereed)
    Abstract [en]

    An ab initio study of the role of electronic curve crossing in the photodissociation dynamics of the alkyl halides is presented. Recent experimental studies show that curve crossing plays a deterministic role in deciding the channel of dissociation. Coupled repulsive potential energy curves of the low-lying n-sigma* states are studied including spin-orbit and relativistic effects. Basis set including effect of core correlation is used. Ab initio vertical excitation spectra of CH3I and CF3I are in agreement with the experimental observation. The curve crossing region is around 2.371 Angstrom for CH3I and CF3I. The potential curves of the repulsive excited states have larger slope for CF3I, suggesting a higher velocity and decreased intersystem crossing probability on fluorination. We also report the potential curves and the region of curve crossing for CH3Br and CH3Cl.

  • 2. Al-Abdalla, A
    et al.
    Barandiaran, Z
    Seijo, L
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Ab initio model potential embedded-cluster study of the ground and lowest excited states of Cr3+ defects in the elpasolites Cs2NaYCl6 and Cs2NaYBr61998In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 108, p. 2005-2014Article in journal (Refereed)
    Abstract [en]

    In this paper we present the results of an ab initio model potential (AIMP) embedded-cluster study of the ground and lowest excited states of Cr3+ defects in the elpasolites Cs2NaYCl6 and Cs2NaYBr6; complete active space SCF (CASSCF) and averaged coupled-pair functional (ACPF) calculations are performed on CrCl63- and CrBr63- clusters embedded in ab initio model potential representations of the surrounding lattices Cs2NaYCl6 and Cs2NaYBr6. The experimental structural data are revisited and some new results are found which differ significantly from those available in the literature. The calculated local structure parameters and electronic transition energies which can be compared to experiments are found to be very good; new structural and spectroscopic results are produced which have been neither measured nor calculated, which are complementary to the available ones, and whose quality is expected to be high as well. In particular, the question of the competition of the excited-state absorptions with the potential vibronic laser emission has been adressed: A considerable overlap between the broad E-2(g) –> (2)A(1g) excited-state absorption and (4)A(2g) <– T-4(2g) emission bands is predicted in both materials, which must result in a reduction in the emission efficiency. Finally, it is shown that the quantum mechanical embedding effects due to the fact that the external Cs+, Na+, Y3+, Cl-, and Br- ions are not point charges, are non-negligible; lacking of these effects must be one of the reasons which make previous Density Functional Theory calculations show significantly larger discrepancies with the available experiments.

  • 3. Andrews, Lester
    et al.
    Wang, Xuefeng
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Bjoern O
    Marsden, Colin J.
    Simple N UF3 and P UF3 molecules with triple bonds to uranium2008In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 29, p. 5366-5370Article in journal (Refereed)
  • 4.
    Aquilante, Francesco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Carlson, Rebecca K.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Delcey, Mickael G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    De Vico, Luca
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen O, Denmark..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ferre, Nicolas
    Univ Aix Marseille, CNRS, Inst Chim Radicalaire, Campus Etoile St Jerome Case 521,Ave Esc, F-13397 Marseille 20, France..
    Frutos, Luis Manuel
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Gagliardi, Laura
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy.;Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Giussani, Angelo
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Hoyer, Chad E.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Li Manni, Giovanni
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Lischka, Hans
    Texas Tech Univ, Dept Chem & Biochem, Mem Circle & Boston, Lubbock, TX 79409 USA.;Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Ma, Dongxia
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Malmqvist, Per Ake
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Mueller, Thomas
    Forschungszentrum Julich, IAS, JSC, Wilhelm Johnen Str, D-52425 Julich, Germany..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, 141 Overman Hall, Bowling Green, OH 43403 USA.;Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam, IL-91904 Jerusalem, Israel..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, POB 1033 Blindern, N-0315 Oslo, Norway..
    Peng, Daoling
    S China Normal Univ, Coll Chem & Environm, Guangzhou 510006, Guangdong, Peoples R China..
    Plasser, Felix
    Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Pritchard, Ben
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Reiher, Markus
    ETH, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Rivalta, Ivan
    Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Schapiro, Igor
    Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France..
    Segarra-Marti, Javier
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Truhlar, Donald G.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Ungur, Liviu
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Valentini, Alessio
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Vancoillie, Steven
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Veryazov, Valera
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Vysotskiy, Victor P.
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Weingart, Oliver
    Univ Dusseldorf, Inst Theoret Chem & Computerchem, Univ Str 1, D-40225 Dusseldorf, Germany..
    Zapata, Felipe
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, p. 506-541Article in journal (Refereed)
    Abstract [en]

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

  • 5. Aquilante, Francesco
    et al.
    Boman, Linus
    Boström, Jonas
    Koch, Henrik
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Sánchez de Merás, Alfredo
    Pedersen, Thomas Bondo
    Cholesky decomposition techniques in electronic structure theory2011In: Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications / [ed] R. Zalesny, P. Mezey, M. G. Papadopoulos and J. Leszczynski, Springer, 2011, p. 301-304Chapter in book (Other academic)
    Abstract [en]

    We review recently developed methods to efficiently utilize the Cholesky decomposition technique in electronic structure calculations. The review starts with a brief introduction to the basics of the Cholesky decomposition technique. Subsequently, examples of applications of the technique to ab inito procedures are presented. The technique is demonstrated to be a special type of a resolution-of-identity or density-fitting scheme. This is followed by explicit examples of the Cholesky techniques used in orbital localization, computation of the exchange contributionto the Fock matrix, in MP2, gradient calculations, and so-called method specific Cholesky decomposition. Subsequently, examples of calibration of the method with respect to computed total energies, excitation energies, and auxiliary basis set pruning are presented. In particular, it is demonstrated that the Cholesky method is an unbiased method to derive auxiliary basis sets. Furthermore, details of the implementational considerations are put forward and examples from a parallel Cholesky decomposition scheme is presented. Finally, an outlook and perspectives are presented, followed by a summary and conclusions section. We are of the opinion that the Cholesky decomposition method is a technique that has been overlooked for too long. We have just recently started to understand how to efficiently incorporate the method in existing ab initio programs. The full potential of the Cholesky technique has not yet been fully explored.

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

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

  • 7.
    Aquilante, Francesco
    et al.
    Univ Bologna, Dipartimento Chim G Ciamician, Bologna, Italy..
    Delcey, Mickael G.
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 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, Oslo, Norway..
    Fernández Galván, Ignacio
    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. Uppsala Univ, Dept Chem Angstrom, Theoret Chem Programme, Uppsala, Sweden..
    Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 2052-2064Article in journal (Refereed)
    Abstract [en]

    The density-fitting technique for approximating electron-repulsion integrals relies on the quality of auxiliary basis sets. These are commonly obtained through data fitting, an approach that presents some shortcomings. On the other hand, it is possible to derive auxiliary basis sets by removing elements from the product space of both contracted and primitive orbitals by means of a particular form of inner projection technique that has come to be known as Cholesky decomposition (CD). This procedure allows for on-the-fly construction of auxiliary basis sets that may be used in conjunction with any quantum chemical method, i.e. unbiased auxiliary basis sets. One key feature of these sets is that they represent the electron-repulsion integral matrix in atomic orbital basis with an accuracy that can be systematically improved. Another key feature is represented by the fact that locality of fitting coefficients is obtained even with the long-ranged Coulomb metric, as result of integral accuracy. Here we report on recent advances in the development of the CD-based density fitting technology. In particular, the implementation of analytical gradients algorithms is reviewed and the present status of local formulations - potentially linear scaling - is analysed in detail.

  • 8. Aquilante, Francesco
    et al.
    Gagliardi, Laura
    Pedersen, Thomas Bondo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, p. 154107-Article in journal (Refereed)
    Abstract [en]

    Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante , J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

  • 9. Aquilante, Francesco
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Pedersen, Thomas Bondo
    Analytic derivatives for the Cholesky representation of the two-electron integrals2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 3, p. 034106-Article in journal (Refereed)
    Abstract [en]

    We propose a formalism for calculating analytic derivatives of the electronic energy with respect to nuclear coordinates using Cholesky decomposition of the two-electron integrals. The formalism is derived by exploiting the equivalence of Cholesky decomposition and density fitting when a suitable auxiliary basis set is used for expanding atomic orbital product densities in the latter. An implementation of gradients at the nonhybrid density functional theory level is presented, and sample calculations demonstrate that the errors in equilibrium geometries due to the Cholesky representation of the integrals can be controlled by adjusting the decomposition threshold.

  • 10. Aquilante, Francesco
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Pedersen, Thomas Bondo
    Unbiased auxiliary basis sets for accurate two-electron integral approximations2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 11, p. 114107-Article in journal (Refereed)
    Abstract [en]

    We propose Cholesky decomposition (CD) of the atomic two-electron integral matrix as a robust and general technique for generating auxiliary basis sets for the density fitting approximation. The atomic CD (aCD) auxiliary basis set is calculated on the fly and is not biased toward a particular quantum chemical method. Moreover, the accuracy of the aCD basis set can be controlled with a single parameter.

  • 11. Aquilante, Francesco
    et al.
    Pedersen, Thomas Bondo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Low-cost evaluation of the exchange Fock matrix from Cholesky and density fitting representations of the electron repulsion integrals2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 126, no 19, p. 194106-Article in journal (Refereed)
    Abstract [en]

    The authors propose a new algorithm, “local K” (LK), for fast evaluation of the exchange Fock matrix in case the Cholesky decomposition of the electron repulsion integrals is used. The novelty lies in the fact that rigorous upper bounds to the contribution from each occupied orbital to the exchange Fock matrix are employed. By formulating these inequalities in terms of localized orbitals, the scaling of computing the exchange Fock matrix is reduced from quartic to quadratic with only negligible prescreening overhead and strict error control. Compared to the unscreened Cholesky algorithm, the computational saving is substantial for systems of medium and large sizes. By virtue of its general formulation, the LK algorithm can be used also within the class of methods that employ auxiliary basis set expansions for representing the electron repulsion integrals.

  • 12. Aquilante, Francesco
    et al.
    Pedersen, Thomas Bondo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn Olof
    De Merás, Alfredo Sánchez
    Koch, Henrik
    Accurate ab initio density fitting for multiconfigurational self-consistent field methods2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 2, p. 024113-Article in journal (Refereed)
    Abstract [en]

    Using Cholesky decomposition and density fitting to approximate the electron repulsion integrals, an implementation of the complete active space self-consistent field (CASSCF) method suitable for large-scale applications is presented. Sample calculations on benzene, diaquo-tetra-mu-acetato-dicopper(II), and diuraniumendofullerene demonstrate that the Cholesky and density fitting approximations allow larger basis sets and larger systems to be treated at the CASSCF level of theory with controllable accuracy. While strict error control is an inherent property of the Cholesky approximation, errors arising from the density fitting approach are managed by using a recently proposed class of auxiliary basis sets constructed from Cholesky decomposition of the atomic electron repulsion integrals.

  • 13.
    Aquilante, Francesco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pedersen, Thomas Bondo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Veryazov, Valera
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    MOLCAS—a software for multiconfigurational quantum chemistry calculations2013In: Wiley Interdisciplinary Reviews: Computational Molecular Science, ISSN 1759-0876, Vol. 3, no 2, p. 143-149Article in journal (Refereed)
    Abstract [en]

    At variance, with most of the quantum chemistry software presently available, MOLCAS is a package that is specialized in multiconfigurational wave function theory (MC-WFT) rather than density functional theory (DFT). Given the much higher algorithmic complexity of MC-WFT versus DFT, an extraordinary effort needs to be made from the programming point of view to achieve state-of-the-art performance for large-scale calculations. In particular, a robust and efficient implementation of the Cholesky decomposition techniques for handling two-electron integrals has been developed which is unique to MOLCAS. Together with this 'Cholesky infrastructure', a powerful and multilayer graphical and scripting user interface is available, which is an essential ingredient for the setup of MC-WFT calculations. These two aspects of the MOLCAS software constitute the focus of the present report.

  • 14.
    Aspuru-Guzik, Alan
    et al.
    Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA.;Canadian Inst Adv Res CIFAR, Toronto, ON M5G 1Z8, Canada..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala Univ, Theoret Chem Programme, Dept CUppsala Univ, Uppsala Ctr Computat Chem UC3, Box 518, S-75120 Uppsala, Sweden..
    Reiher, Markus
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    The Matter Simulation (R)evolution2018In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 2, p. 144-152Article in journal (Refereed)
    Abstract [en]

    To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, and robotics. This drives us to consider the future of computer simulation of matter from the molecular to the human length and time scales in a radical way that deliberately dares to go beyond the foreseeable next steps in any given discipline. This perspective article presents a view on this future development that we believe is likely to become a reality during our lifetime.

  • 15.
    Atsumi, Michiko
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Gonzalez, Leticia
    Gourlaouen, Christophe
    Daniel, Chantal
    Ab initio and DFT analysis of the low-lying electronic states of metal dihalides: quantum chemical calculations on the neutral BrMCl (M = Cu, Ag, Au)2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 25, p. 10151-10157Article in journal (Refereed)
    Abstract [en]

    The electronic configuration of the electronic ground and low-lying doublet excited states of neutral metal dihalides BrMCl (M = Cu, Ag, Au) has been investigated on the basis of CASSCF/CASPT2 methods taking into account scalar relativistic effects. A preliminary study of the electronic problem in BrAgCl, based on DFT and CASSCF/CASPT2 approaches and using various basis sets, namely relativistic all-electron basis sets, effective core potentials and ab initio model potentials (AIMP), as well as non-relativistic AIMP is discussed. It is shown that single-determinant methods are not flexible enough to describe the bonding of the neutral species in the electronic ground state regardless of the basis set. The failure to allocate the single electron of BrAgCl correlates with a wrong charge distribution within the complex, which is more accentuated when using pseudopotential basis sets. The inclusion of static and dynamic correlation effects by means of CASSCF/CASPT2 methods using large relativistic all-electron basis sets provides a correct qualitative picture of the electronic structure of the BrMCl series (M = Cu, Ag, Au). The spin unrestricted KS-DFT approach leads to a reasonable description of the degenerate electronic ground state ((2)Sigma/(2)Pi) bonding in these complexes with negligible spin contamination providing comparative spin densities in the series of molecules under investigation.

  • 16.
    Augusto, Felipe A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, Av Prof Lineu Prestes 748, Sao Paulo, Brazil..
    Francés-Monerris, Antonio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    Fdez. Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuán, Daniel
    Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    Bastos, Erick L.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, Av Prof Lineu Prestes 748, Sao Paulo, Brazil..
    Baader, Wilhelm J.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, Av Prof Lineu Prestes 748, Sao Paulo, Brazil..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Mechanism of activated chemiluminescence of cyclic peroxides: 1,2-dioxetanes and 1,2-dioxetanones2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 5, p. 3955-3962Article in journal (Refereed)
    Abstract [en]

    Almost all chemiluminescent and bioluminescent reactions involve cyclic peroxides. The structure of the peroxide and reaction conditions determine the quantum efficiency of light emission. Oxidizable fluorophores, the so-called activators, react with 1,2-dioxetanones promoting the former to their first singlet excited state. This transformation is inefficient and does not occur with 1,2-dioxetanes; however, they have been used as models for the efficient firefly bioluminescence. In this work, we use the SA-CASSCF/CASPT2 method to investigate the activated chemiexcitation of the parent 1,2-dioxetane and 1,2-dioxetanone. Our findings suggest that ground state decomposition of the peroxide competes efficiently with the chemiexcitation pathway, in agreement with the available experimental data. The formation of non-emissive triplet excited species is proposed to explain the low emission efficiency of the activated decomposition of 1,2-dioxetanone. Chemiexcitation is rationalized considering a peroxide/activator supermolecule undergoing an electron-transfer reaction followed by internal conversion.

  • 17. Barnes, Leslie A
    et al.
    Lie, Bowen
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Structure and energetics of Cr(CO)6 and Cr(CO)51993In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 98, no 5, p. 3978-3989Article in journal (Refereed)
    Abstract [en]

    The geometric structure of Cr(CO)6 is optimized at the modified coupled-pair functional (MCPF), single and double excitation coupled-cluster (CCSD), and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD, and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD, and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used here and in a previous study. Calculations using larger basis sets reduce the BSSE, but the total binding energy of Cr(CO)6 is Still Significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. In the largest basis set, the total CO binding energy of Cr(CO)6 is estimated to be 140 kcal/mol at the CCSD(T) level of theory, or about 86% of the experimental value. The remaining discrepancy between the experimental and theoretical value is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular, an additional d function and an f function on each C and 0 are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive set (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

  • 18. Barnes, Leslie A
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Symmetry breaking in O+4: an application of the Brueckner coupled-cluster method1994In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 223, no 3, p. 207-214Article in journal (Refereed)
    Abstract [en]

    A recent calculation of the antisymmetric stretch frequency for the rectangular structure of quartet O4+ using the QCISD(T) method gave a value of 3710 cin-1. This anomalous frequency is shown to be a consequence of symmetry-breaking effects, which occur even though the QCISD(T) solution derived from a delocalized SCF reference function lies energetically well below the two localized (symmetry-broken) solutions at the equilibrium geometry. The symmetry breaking is almost eliminated at the CCSD level of theory, but the small remaining symmetry-breaking effects are magnified at the CCSD (T) level of theory so that the antisymmetric stretch frequency is still significantly in error. The Brueckner coupled-cluster method, however, leads to a symmetrical solution which is free of symmetry-breaking effects, with an antisymmetric stretch frequency of 1322 cm-1, in good agreement with our earlier calculations using the CASSCF/CASSI method.

  • 19. Barnes, Leslie A
    et al.
    Liu, Bowen
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Bond length, dipole moment, and harmonic frequency of CO1993In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 98, no 5, p. 3972-3977Article in journal (Refereed)
    Abstract [en]

    A detailed comparison of some properties of CO is given, at the modified coupled-pair functional, single and double excitation coupled-cluster (CCSD), and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), using a variety of basis sets. With very large one-particle basis sets, the CCSD(T) method gives excellent results for the bond distance, dipole moment, and harmonic frequency of CO. In a [6s 5p 4d 3f 2g 1h] + (1s 1p 1d) basis set, the bond distance is about 0.005a0 too large, the dipole moment about 0.005 a.u. too small, and the frequency about 6 cm-1 too small, when compared with experimental results.

  • 20. Barone, Giampaolo
    et al.
    Mastalerz, Remigius
    Reiher, Markus
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Nuclear quadrupole moment of Sn-1192008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 7, p. 1666-1672Article in journal (Refereed)
    Abstract [en]

    Second-order scalar-relativistic Douglas-Kroll-Hess density functional calculations of the electric field gradient, including an analytic correction of the picture change error, were performed for 34 tin compounds of which molecular structures and Sn-119 Mossbauer spectroscopy parameters are experimentally known. The components of the diagonalized electric field gradient tensor, V-xx,V-yy, V-zz, were used to determine the quantity V, which is proportional to the nuclear quadrupole splitting parameter Delta E. The slope of the linear correlation plot of the experimentally determined Delta E parameter versus the corresponding calculated V data allowed us to obtain an absolute value of the nuclear quadrupole moment Q of Sn-119 equal to Q = 13.2 +/- 0.1 fm(2). This is about 11% larger than the picture-change-error-affected value and in good agreement with previous estimates of the picture change error in compounds of similar atomic charge. Moreover, despite the variety of the tin compounds considered in this study, the new result is in excellent agreement with the previously determined most accurate value of Q for Sn-119 of Q = 12.8 +/- 0.7 fm(2), but with a noticeably narrower error bar. The reliability of the calibration method in the calculation of the Delta E parameter of tin compounds is within a margin of +/- 0.3 mm s(-1) when compared to experimental data and does not depend on the inclusion of the picture change correction in the density functional calculations but is essentially determined by the use of an atomic natural orbital relativistic core-correlated basis set for the description of the core electron density. The results obtained suggest that the present picture-change-corrected Douglas-Kroll-Hess approach provides reliable electric field gradients in the case of closed-shell metal compounds involving elements up to the fifth row of the periodic table for which spin-orbit coupling is negligible.

  • 21. Bernhardsson, Anders
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Karlström, Gunnar
    Roos, Björn O
    Direct self-consistent reaction field with Pauli repulsion: Solvation effects on methylene peroxide1996In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 251, no 3-4, p. 141-149Article in journal (Refereed)
    Abstract [en]

    The properties of methylene peroxide in the gas phase and water have been examined. The solution effects have been modeled with a cavity. To make it possible to optimize the geometry of the cavity, we have added an approximate description of the Pauli repulsion between the solvent and the solute. An efficient direct implementation of the calculation of multicenter multipole operators is also described. We have applied the method to calculate the electric properties of methylene peroxide, a system that is characterized by its near degeneracy between a biradical and a zwitterionic state. As expected, it is shown that solvent effects will stabilize the ionic configuration, resulting in a considerably weakened OO bond and an increased double bond character in the CO bond. The theoretical study has been performed using the multiconfigurational (CAS) SCF method and second-order perturbation theory (CASPT2).

  • 22. Bernhardsson, Anders
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Olsen, Jeppe
    Fülscher, Markus
    A direct implementation of the second-order derivatives of multiconfigurational SCF energies and an analysis of the preconditioning in the associated response equation1999In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 96, no 4, p. 617-628Article in journal (Refereed)
    Abstract [en]

    A direct implementation of the reduced multiplication scheme of the Rys-Gauss quadrature in the computation of the second-order geometric derivatives for MCSCF wavefunctions is presented. Characteristics unique to this implementation are simultaneous evaluation of first- and second-order two-electron integral derivatives, compact representation of intermediate elements and efficient prescreening. Finally, a novel technique for the preconditioning of the response equations is reported. Applications sizing up to 510 basis functions are included in the presentation.

  • 23.
    Berraud-Pache, Romain
    et al.
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Navizet, Isabelle
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 20, p. 5173-5182Article in journal (Refereed)
    Abstract [en]

    The bioluminescence emission from fireflies is an astounding tool to mark and view cells. However, the bioluminescent mechanism is not completely deciphered, limiting the comprehension of key processes. We use a theoretical approach to study for the first time the arrival of a dioxygen molecule inside the fireflies protein and one path of the formation of the dioxetanone ring, the high-energy intermediate precursor of the bioluminescence. To describe this reaction step, a joint approach combining classical molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations is used. The formation of the dioxetanone ring has been studied for both singlet and triplet states with the help of MS-CASPT2 calculations. We also emphasize the role played by the proteinic environment in the formation of the dioxetanone ring. The results obtained shed some light on an important reaction step and give new insights concerning the bioluminescence in fireflies.

  • 24. 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.

  • 25. 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.

  • 26. 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.

  • 27. 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.

  • 28. Boström, Jonas
    et al.
    Veryazov, Valera
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Bondo Pedersen, Thomas
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical gradients of the second-order Møller–Plesset energy using Cholesky decompositions2014In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 114, no 5, p. 321-327Article in journal (Refereed)
    Abstract [en]

    An algorithm for computing analytical gradients of the second-order Møller–Plesset (MP2) energy using density fitting (DF) is presented. The algorithm assumes that the underlying canonical Hartree–Fock reference is obtained with the same auxiliary basis set, which we obtain by Cholesky decomposition (CD) of atomic electron repulsion integrals. CD is also used for the negative semidefinite MP2 amplitude matrix. Test calculations on the weakly interacting dimers of the S22 test set (Jurečka et al., Phys. Chem. Chem. Phys. 2006, 8, 1985) show that the geometry errors due to the auxiliary basis set are negligible. With double-zeta basis sets, the error due to the DF approximation in intermolecular bond lengths is better than 0.1 pm. The computational time is typically reduced by a factor of 6–7.

  • 29. Chen, Shu-Feng
    et al.
    Liu, Ya-Jun
    Liu, Feng-Yi
    De Vico, Luca
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Multireference calculations on the chemical origin and mechanism of firefly bioluminescence2010In: Abstracts of the 16th International Symposium on Bioluminescence and Chemiluminescence – (ISBC 2010): [Published in: Luminescence 2010; 25: 81–216], 2010, Vol. 25, no 2, p. 89-90Conference paper (Other academic)
  • 30. 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-.

  • 31. Chen, Shufeng
    et al.
    Navizet, Isabelle
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Liu, Yajun
    Ferre, Nicolas
    Bioluminescence of Obelin: identification of the light emitters using QM/MM models2014In: Luminescence (Chichester, England Print), ISSN 1522-7235, E-ISSN 1522-7243, Vol. 29, p. 19-19Article in journal (Other academic)
  • 32. Chen, Shufeng
    et al.
    Navizet, Isabelle
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Liu, Yajun
    Ferre, Nicolas
    Hybrid QM/MM Simulations of the Obelin Bioluminescence and Fluorescence Reveal an Unexpected Light Emitter2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 11, p. 2896-2903Article in journal (Refereed)
    Abstract [en]

    Obelia longissima, a tiny hydrozoan living in temperate and cold seas, features the Obelin photoprotein, which emits blue light. The Obelin bioluminescence and the Ca2+-discharged Obelin fluorescence spectra show multimodal characteristics that are currently interpreted by the concomitant participation of several light emitters. Up to now, the coelenteramide luminophore is thought to exist in different protonation states, one of them engaged in an ion-pair with the nearby residue, His22. Using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, we demonstrate that such an ion-pair cannot exist as a stable light emitter. However, when His22 electric neutrality is maintained by means of another proton transfer, the phenolate state of coelenteramide exhibits emission properties in agreement with experiment. Finally, an alternative nonradiative decay pathway, involving the formation of a diradical excited state, is postulated for the first time.

  • 33. 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.

  • 34. Chen, Shu-Feng
    et al.
    Yue, Ling
    Liu, Ya-Jun
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Multireference theoretical studies on the solvent effect of firefly multicolor bioluminescence2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 13, p. 3371-3377Article in journal (Refereed)
    Abstract [en]

    In concert with the recent spectroscopic studies of the light-color modulation mechanism of firefly (Hirano et al., J Am Chem Soc 2009, 131, 2385), quantum chemical calculations using complete active space SCF (CASSCF), multistate complete active space second order perturbation (MS-CASPT2) theory as well as a time-dependent density functional theory (TD-DFT) approach with the Coulomb attenuated hybrid exchange-correlation functional (CAM-B3LYP) were performed on the excited state (S1) of the keto-form oxyluciferin (keto-OxyLH2). Benzene, DMSO, CH3CN, and H2O were chosen as polar solvents. The polarization effect of less polar solvent was considered by a simple model, complex of keto-OxyLH2, and NH3 with different covalent character. The calculated results supported the experimental conclusion: (1) the light emitter of bioluminescence is the S1 state of keto-OxyLH2 anion [(keto-1)*], and (2) light emission from (keto-1)* is modulated by the polarity of surrounding environment and the degree of covalent character of hydrogen bond between (keto-1)* and a protonated basic moiety. The mechanism of the multicolor bioluminescence was discussed from the theoretical viewpoint.

  • 35. Choe, Yong-Kee
    et al.
    Nakajima, Takahito
    Hirao, Kimihiko
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Theoretical study of the electronic ground state of iron(II) porphine. II1999In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 111, no 9, p. 3837-3845Article in journal (Refereed)
    Abstract [en]

    Ten low-lying electronic states of Fe(II) porphine, (5)A(1g), E-5(g), B-5(2g), (3)A(2g), B-3(2g), E-3(g)(A), E-3(g)(B), (1)A(1g), B-1(2g), and E-1(g) states, are studied with multiconfigurational second-order perturbation (CASPT2) calculations with complete active space self-consistent field (CASSCF) reference functions with larger active space and basis sets. The enlargement of active space and basis sets has no influence on the conclusion of a previous multireference Moller-Plesset perturbation (MRMP) study. The present CASPT2 calculation concludes that the (5)A(1g) state is the ground state. A relativistic correction has been performed by the relativistic scheme of eliminating small components (RESC). For energetics, no significant contribution from the relativistic correction was found. The relative energies and orbital energies are not changed appreciably by the introduction of a relativistic correction. The present result does not agree with all the spectroscopic observations, but is consistent with a magnetic moment study.

  • 36. Chwee, Tsz S
    et al.
    Szilva, Andrew B
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Carter, Emily A
    Linear scaling multireference singles and doubles configuration interaction2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 22, p. 224106-Article in journal (Refereed)
    Abstract [en]

    A linear scaling multireference singles and doubles configuration interaction (MRSDCI) method has been developed. By using localized bases to span the occupied and virtual subspace, local truncation schemes can be applied in tandem with integral screening to reduce the various bottlenecks in a MRSDCI calculation. Among these, the evaluation of electron repulsion integrals and their subsequent transformation, together with the diagonalization of the large CI Hamiltonian matrix, correspond to the most computationally intensive steps in a MRSDCI calculation. We show that linear scaling is possible within each step. The scaling of the method with system size is explored with a system of linear alkane chains and we proceed to demonstrate this method can produce smooth potential energy surfaces via calculating the dissociation of trans-6-dodecene (C12H24) along the central C=C bond.

  • 37. de Jong, Wibe A
    et al.
    Bylaska, Eric
    Govind, Niranjan
    Janssen, Curtis L
    Kowalski, Karol
    Müller, Thomas
    Nielsen, Ida M B
    van Dam, Hubertus J J
    Veryazov, Valera
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Utilizing high performance computing for chemistry: parallel computational chemistry2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 26, p. 6896-6920Article in journal (Refereed)
    Abstract [en]

    Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.

  • 38. 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.

  • 39. De Vico, Luca
    et al.
    Liu, Ya-Jun
    Krogh, Jesper Wisborg
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Chemiluminescence of 1,2-dioxetane. Reaction mechanism uncovered2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 32, p. 8013-8019Article in journal (Refereed)
    Abstract [en]

    The thermal decomposition of 1,2-dioxetane and the associated production of chemiluminescent products, model for a wide range of chemiluminescent reactions, has been studied at the multistate multiconfigurational second-order perturbation level of theory. This study is in qualitative and quantitative agreement with experimental observations with respect to the activation energy and the observed increase of triplet and singlet excited products as substituents are added to the parent molecule. The, previously incomplete, reaction mechanism of the chemiluminescence of 1,2-dioxetane is now rationalized and described as mainly due to a particular form of entropic trapping.

  • 40. 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.

  • 41.
    Delcey, Mickael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aquilante, Francesco
    Pedersen, Thomas B.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical CD/RI-SA-CASSCF gradients: Implementation and performance2014In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 248Article in journal (Other academic)
  • 42.
    Delcey, Mickaël G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Freitag, Leon
    Pedersen, Thomas Bondo
    Aquilante, Francesco
    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.
    Gonzalez, Leticia
    Analytical gradients of complete active space self-consistent field energies using Cholesky decomposition: Geometry optimization and spin-state energetics of a ruthenium nitrosyl complex2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 17, p. 174103-Article in journal (Refereed)
    Abstract [en]

    We present a formulation of analytical energy gradients at the complete active space self-consistent field (CASSCF) level of theory employing density fitting (DF) techniques to enable efficient geometry optimizations of large systems. As an example, the ground and lowest triplet state geometries of a ruthenium nitrosyl complex are computed at the DF-CASSCF level of theory and compared with structures obtained from density functional theory (DFT) using the B3LYP, BP86, and M06L functionals. The average deviation of all bond lengths compared to the crystal structure is 0.042 angstrom at the DF-CASSCF level of theory, which is slightly larger but still comparable with the deviations obtained by the tested DFT functionals, e. g., 0.032 angstrom with M06L. Specifically, the root-mean-square deviation between the DF-CASSCF and best DFT coordinates, delivered by BP86, is only 0.08 angstrom for S-0 and 0.11 angstrom for T-1, indicating that the geometries are very similar. While keeping the mean energy gradient errors below 0.25%, the DF technique results in a 13-fold speedup compared to the conventional CASSCF geometry optimization algorithm. Additionally, we assess the singlet-triplet energy vertical and adiabatic differences with multiconfigurational second-order perturbation theory (CASPT2) using the DF-CASSCF and DFT optimized geometries. It is found that the vertical CASPT2 energies are relatively similar regardless of the geometry employed whereas the adiabatic singlet-triplet gaps are more sensitive to the chosen triplet geometry. (C) 2014 AIP Publishing LLC.

  • 43.
    Delcey, Mickaël G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Linguerri, R.
    Hochlaf, M.
    Francisco, J. S.
    Communication: Theoretical prediction of the structure and spectroscopic properties of the X∼ and A∼ states of hydroxymethyl peroxy (HOCH2OO) radical2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, no 2, p. 021105-Article in journal (Refereed)
    Abstract [en]

    The hydroxymethyl peroxy (HMOO) radical is a radical product from the oxidation of non-methane hydrocarbons. The present study provides theoretical prediction of critical spectroscopic features of this radical that should aid in its experimental characterization. Structure, rotational constants, and harmonic frequencies are presented for the ground and first excited electronic states of HMOO. The adiabatic transition energy for the A←X process is 7360 cm-1, suggesting that this transition, occurring in the mid to near infrared, is the most promising candidate for observing the radical spectroscopically. The band origin of the A←X transition of HMOO is calibrated and benchmarked with the corresponding state of the HOO radical, which is experimentally and theoretically well characterized.

  • 44.
    Delcey, Mickaël G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pedersen, Thomas Bondo
    University of Oslo.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Università di Bologna.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical gradients of the state-average complete active space self-consistent field method with density fitting2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 4, article id 044110Article in journal (Refereed)
    Abstract [en]

    An efficient implementation of the state-averaged complete active space self-consistent field (SA-CASSCF) gradients employing density fitting (DF) is presented. The DF allows a reduction both in scaling and prefactors of the different steps involved. The performance of the algorithm is demonstrated on a set of molecules ranging up to an iron-Heme b complex which with its 79 atoms and 811 basis functions is to our knowledge the largest SA-CASSCF gradient computed. For smaller systems where the conventional code could still be used as a reference, both the linear response calculation and the gradient formation showed a clear timing reduction and the overall cost of a geometry optimization is typically reduced by more than one order of magnitude while the accuracy loss is negligible.

  • 45.
    Delcey, Mickaël G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pierloot, Kristine
    Phung, Quan M.
    Vancoillie, Steven
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ryde, Ulf
    Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 17, p. 7927-7938Article in journal (Refereed)
    Abstract [en]

    We have studied the geometry and singlet-triplet energy difference of two mono-nuclear Ni2+ models related to the active site in [NiFe] hydrogenase. Multiconfigurational second-order perturbation theory based on a complete active-space wavefunction with an active space of 12 electrons in 12 orbitals, CASPT2(12,12), reproduces experimental bond lengths to within 1 pm. Calculated singlet-triplet energy differences agree with those obtained from coupled-cluster calculations with single, double and (perturbatively treated) triple excitations (CCSD(T)) to within 12 kJ mol(-1). For a bimetallic model of the active site of [NiFe] hydrogenase, the CASPT2(12,12) results were compared with the results obtained with an extended active space of 22 electrons in 22 orbitals. This is so large that we need to use restricted active-space theory (RASPT2). The calculations predict that the singlet state is 48-57 kJ mol(-1) more stable than the triplet state for this model of the Ni-Sl(a) state. However, in the [NiFe] hydrogenase protein, the structure around the Ni ion is far from the square-planar structure preferred by the singlet state. This destabilises the singlet state so that it is only similar to 24 kJ mol(-1) more stable than the triplet state. Finally, we have studied how various density functional theory methods compare to the experimental, CCSD(T), CASPT2, and RASPT2 results. Semi-local functionals predict the best singlet-triplet energy differences, with BP86, TPSS, and PBE giving mean unsigned errors of 12-13 kJ mol(-1) (maximum errors of 25-31 kJ mol(-1)) compared to CCSD(T). For bond lengths, several methods give good results, e. g. TPSS, BP86, and M06, with mean unsigned errors of 2 pm for the bond lengths if relativistic effects are considered.

  • 46. Devarajan, Ajitha
    et al.
    Gaenko, Alexander
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per-Åke
    Role of Electronic Curve Crossing of Benzene S-1 State in the Photodissociation of Aryl Halides, Effect of Fluorination: RASSI-SO MS-CASPT2 Study2009In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 109, no 9, p. 1962-1974Article in journal (Refereed)
    Abstract [en]

    An ab initio study of the role of electronic curve crossing of benzene S-1 state in the photo dissociation dynamics of the iodobenzene and effect of fluorination is presented. Two dissociative life times observed in iodobenzene is attributed to the coupled repulsive potential energy curves of the low-lying n-sigma*, pi-sigma*, pi-pi* states. The direct channel is attributed to the alkyl like transition and the indirect channel is attributed to the mixing of the alkyl like transitions with the low lying benzene pi-pi* transitions. Fluorination of iodobenzene results in a substantial increase in the direct channel product. To analyze the possible role of electronic curve crossing of these transitions, potential energy curves of low-lying n-sigma*, pi-sigma*, pi-pi* states were studied including spin-orbit and relativistic effects using the Restricted Active Space state interaction multistate complete active space perturbation theory (RASSI-MS-CASPT2) method. Crossing behavior of spin-free and spin-orbit potential energy curves was analyzed for the role of the benzene S-1 state. Our results indicate the curve crossing region to be around 2.00-2.35 angstrom for both C6H5I and C6F5I. Analysis of effect of fluorination on the energies of states corresponding to benzene pi-pi* and n-sigma* transitions suggests an increase in the energy of benzene pi-pi* states and a decrease in the energy of the states corresponding to n-sigma* transitions. Increased spin-orbit gap, increased separation of the benzene S-1(pi-pi*) state and n-sigma* states in the region of curve crossing, lesser mixing of the pi-pi* and n-sigma* states, an order of magnitude decrease in the transition strength to the benzene singlet transition all contributed to the observed Substantial increase in the quantum yield of the direct channel product on fluorination of aryl halides.

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

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

  • 48. Engkvist, Ola
    et al.
    Borowski, Piotr
    Bemgård, Agneta
    Karlström, Gunnar
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Colmsjö, Anders
    On the relation between retention indexes and the interaction between the solute and the column in gas-liquid chromatography1996In: Journal of chemical information and computer sciences, ISSN 0095-2338, E-ISSN 1520-5142, Vol. 36, no 6, p. 1153-1161Article in journal (Refereed)
    Abstract [en]

    Gas-liquid chromatography retention indexes for organic molecules are determined by the interaction between the molecule and the column liquid phase. In this article, a model for calculating the interaction energy between a molecule and a dielectric wall is developed. The model is at least to our knowledge the first attempt to predict retention indexes from the interaction between the molecules and the column. This approach to predict retention indexes is radically different from methods proposed before. Earlier predictions of the retention indexes have been done by a large number of descriptors, which were Linearly correlated to the retention indexes. The developed model has been tested for polycyclic aromatic hydrocarbons mainly with a molecular weight of 302. For the molecules with MW 302 the obtained correlation coefficient is 0.92. A somewhat simpler model is used to fit PAH with different MWs. A correlation coefficient of 0.998 is obtained if the retention indexes were fitted to the logarithm of the interaction energies between the PAHs and the column.

  • 49.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Lundberg, Marcus
    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.
    Roca-Sanjuan, Daniel
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 28, p. 18653-18664Article in journal (Refereed)
    Abstract [en]

    Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference multiconfigurational quantum chemistry methods and accurate reaction-path computational strategies were used to determine the reaction coordinate of three successive processes: decomposition of the dioxetane moiety, non-adiabatic energy transfer from the ground to the excited state, and finally non-radiative decay of the 1,3-butadiene group. With the present study, we open a new area of research within computational photochemistry to study chemically-induced excited-state chemistry that is difficult to tackle experimentally due to the short-lived character of the species involved in the process. The findings shall be of relevance to unveil "dark'' photochemistry mechanisms, which might operate in biological systems under conditions of lack of light. These mechanisms might allow reactions that are typical of photo-induced phenomena.

  • 50.
    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.

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