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Publications (10 of 187) Show all publications
Sand, A. M., Hoyer, C. E., Sharkas, K., Kidder, K. M., Lindh, R., Truhlar, D. G. & Gagliard, L. (2018). Analytic Gradients for Complete Active Space Pair-Density Functional Theory. Journal of Chemical Theory and Computation, 14(1), 126-138
Open this publication in new window or tab >>Analytic Gradients for Complete Active Space Pair-Density Functional Theory
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 1, p. 126-138Article in journal (Refereed) Published
Abstract [en]

Analytic gradient routines are a desirable feature for quantum mechanical methods, allowing for efficient determination of equilibrium and transition state structures and several other molecular properties. In this work, we present analytical gradients for multiconfiguration pair-density functional theory (MC-PDFT) when used with a state-specific complete active space self-consistent field reference wave function. Our approach constructs a Lagrangian that is variational in all wave function parameters. We find that MC-PDFT locates equilibrium geometries for several small- to medium-sized organic molecules that are similar to those located by complete active space second-order perturbation theory but that are obtained with decreased computational cost.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-341587 (URN)10.1021/acs.jctc.7b00967 (DOI)000419998300012 ()29211966 (PubMedID)
Funder
Swedish Research Council, 2016-03398
Available from: 2018-02-12 Created: 2018-02-12 Last updated: 2018-02-12Bibliographically approved
Tamayo-Mendoza, T., Kreisbeck, C., Lindh, R. & Aspuru-Guzik, A. (2018). Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock. ACS CENTRAL SCIENCE, 4(5), 559-566
Open this publication in new window or tab >>Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock
2018 (English)In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 5, p. 559-566Article in journal (Refereed) Published
Abstract [en]

Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult, a Hartree-Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-358092 (URN)10.1021/acscentsci.7b00586 (DOI)000434851700009 ()29806002 (PubMedID)
Funder
Swedish Research Council, 2016-03398
Available from: 2018-08-24 Created: 2018-08-24 Last updated: 2018-08-24Bibliographically approved
Berraud-Pache, R., Lindh, R. & Navizet, I. (2018). QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion. Journal of Physical Chemistry B, 122(20), 5173-5182
Open this publication in new window or tab >>QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion
2018 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 20, p. 5173-5182Article in journal (Refereed) Published
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.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-357566 (URN)10.1021/acs.jpcb.8b00642 (DOI)000433403500005 ()29659277 (PubMedID)
Funder
Swedish Research Council, 2016-03398
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved
Aspuru-Guzik, A., Lindh, R. & Reiher, M. (2018). The Matter Simulation (R)evolution. ACS CENTRAL SCIENCE, 4(2), 144-152
Open this publication in new window or tab >>The Matter Simulation (R)evolution
2018 (English)In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 2, p. 144-152Article in journal (Refereed) Published
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.

National Category
Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-351271 (URN)10.1021/acscentsci.7b00550 (DOI)000426613700006 ()
Funder
Swedish Research Council, 2016-03398
Available from: 2018-06-04 Created: 2018-06-04 Last updated: 2018-06-04Bibliographically approved
Head-Gordon, M. & Lindh, R. (2017). A celebration of the Swedish school. Molecular Physics, 115(17-18), 1993-1994
Open this publication in new window or tab >>A celebration of the Swedish school
2017 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 1993-1994Article in journal, Editorial material (Other academic) Published
National Category
Theoretical Chemistry Educational Sciences
Identifiers
urn:nbn:se:uu:diva-345650 (URN)10.1080/00268976.2017.1341097 (DOI)000408727700002 ()
Available from: 2018-03-12 Created: 2018-03-12 Last updated: 2018-03-12Bibliographically approved
Roca-Sanjuán, D., Francés-Monerris, A., Fernández Galván, I., Farahani, P., Lindh, R. & Liu, Y.-J. (2017). Advances in computational photochemistry and chemiluminescence of biological and nanotechnological molecules. In: Angelo Albini, Elisa Fasani (Ed.), Photochemistry: Volume 44: (pp. 16-60). Cambridge, UK: Royal Society of Chemistry
Open this publication in new window or tab >>Advances in computational photochemistry and chemiluminescence of biological and nanotechnological molecules
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2017 (English)In: Photochemistry: Volume 44 / [ed] Angelo Albini, Elisa Fasani, Cambridge, UK: Royal Society of Chemistry, 2017, p. 16-60Chapter in book (Other academic)
Abstract [en]

Recent advances (2014–2015) in computational photochemistry and chemiluminescence derive from the development of theory and from the application of state-of-the-art and new methodology to challenging electronic-structure problems. Method developments have mainly focused, first, on the improvement of approximate and cheap methods to provide a better description of non-adiabatic processes, second, on the modification of accurate methods in order to decrease the computation time and, finally, on dynamics approaches able to provide information that can be directly compared with experimental data, such as yields and lifetimes. Applications of the ab initio quantum-chemistry methods have given rise to relevant findings in distinct fields of the excited-state chemistry. We briefly summarise, in this chapter, the achievements on photochemical mechanisms and chemically-induced excited-state phenomena of interest in biology and nanotechnology.

Place, publisher, year, edition, pages
Cambridge, UK: Royal Society of Chemistry, 2017
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-336863 (URN)10.1039/9781782626954-00016 (DOI)978-1-78262-543-8 (ISBN)
Available from: 2017-12-18 Created: 2017-12-18 Last updated: 2017-12-28
Sørensen, L. K., Guo, M., Lindh, R. & Lundberg, M. (2017). Applications to metal K pre-edges of transitionmetal dimers illustrate the approximate origin independence for the intensities in the length representation. Molecular Physics, 115(1-2), 174-189
Open this publication in new window or tab >>Applications to metal K pre-edges of transitionmetal dimers illustrate the approximate origin independence for the intensities in the length representation
2017 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 1-2, p. 174-189Article in journal (Refereed) Published
Abstract [en]

X-ray absorption spectroscopy (XAS) in the metal K pre-edge is a standard probe of electronic and geometric structure of transition metal complexes. Simulating the K pre-edge spectra requires contributions beyond the electric dipole, but if that term is non-zero, the second-order terms, e. g. electric quadrupoles, are no longer origin-independent. In the velocity representation, complete origin independence can be achieved by including all terms to the same order in the oscillator strength. Here, we implement that approach in the length representation and use it for restricted active space (RAS) simulations of metal K pre-edges of iron monomers and dimers. Complete origin independence is not achieved and the size of the remaining errors depends on the electric dipole oscillator strength and its ratio in length and velocity representations. The error in the origin independence is in the ANO basis sets two orders of magnitude smaller than the value of the individual contributions. For systemswith strong electric dipole contributions, the errors are not significant within 3 angstrom from a metal centre, far enough to handlemany multi-metal systems. Furthermore, we discuss the convergence of the multipole expansion, the possibility to assign spectral contributions, and the origin of negative absorption intensities. [GRAPHICS]

Place, publisher, year, edition, pages
TAYLOR & FRANCIS LTD, 2017
Keywords
Multiconfigurational wavefunction, oscillator strengths, quadrupole intensities, properties, X-ray spectroscopy
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-319774 (URN)10.1080/00268976.2016.1225993 (DOI)000396794700015 ()
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish Research Council, 2012-3910 2012-3924
Available from: 2017-04-12 Created: 2017-04-12 Last updated: 2018-08-14Bibliographically approved
Vacher, M., Brakestad, A., Karlsson, H. O., Fernández Galván, I. & Lindh, R. (2017). Dynamical Insights into the Decomposition of 1,2-Dioxetane. Journal of Chemical Theory and Computation, 13(6), 2448-2457
Open this publication in new window or tab >>Dynamical Insights into the Decomposition of 1,2-Dioxetane
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2017 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 6, p. 2448-2457Article in journal (Refereed) Published
Abstract [en]

Chemiluminescence in 1,2-dioxetane occurs through a thermally activated decomposition reaction into two formaldehyde molecules. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction have been simulated, starting from the first O–O bond-breaking transition structure. The ground-state dissociation occurs between t = 30 fs and t = 140 fs. The so-called entropic trap leads to frustrated dissociations, postponing the decomposition reaction. Specific geometrical conditions are necessary for the trajectories to escape from the entropic trap and for dissociation to be possible. The singlet excited states participate as well in the trapping of the molecule: dissociation including the nonadiabatic transitions to singlet excited states now occurs from t = 30 fs to t = 250 fs and later. Specific regions of the seam of the So/S1 conical intersections that would "retain" the molecule for longer on the excited state have been identified.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-329717 (URN)10.1021/acs.jctc.7b00198 (DOI)000403530100009 ()28437611 (PubMedID)
Funder
Swedish Research Council, 2012-3910
Available from: 2017-10-02 Created: 2017-10-02 Last updated: 2017-10-02Bibliographically approved
Sörensen, L. K., Lindh, R. & Lundberg, M. (2017). Gauge origin independence in finite basis sets and perturbation theory. Chemical Physics Letters, 683, 536-542
Open this publication in new window or tab >>Gauge origin independence in finite basis sets and perturbation theory
2017 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 683, p. 536-542Article in journal (Refereed) Published
Abstract [en]

We show that origin independence in finite basis sets for the oscillator strengths is possibly in any gauge contrary to what is stated in literature. This is proved from a discussion of the consequences in perturbation theory when the exact eigenfunctions and eigenvalues to the zeroth order Hamiltonian H-0 cannot be found. We demonstrate that the erroneous conclusion for the lack of gauge origin independence in the length gauge stems from not transforming the magnetic terms in the multipole expansion leading to the use of a mixed gauge. Numerical examples of exact origin dependence are shown.

Keywords
Gauge origin independence, Finite basis sets, Perturbation theory, Oscillator strengths, X-ray spectroscopy
National Category
Physical Sciences Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-333065 (URN)10.1016/j.cplett.2017.05.003 (DOI)000405802200086 ()
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish Research Council, 2012-3910, 2012-3924Swedish National Infrastructure for Computing (SNIC), snic2014-5-36, snic2015-4-71, snic2015-1-465, snic2015-1427
Available from: 2017-11-09 Created: 2017-11-09 Last updated: 2018-08-14Bibliographically approved
Vacher, M., Farahani, P., Valentini, A., Frutos, L. M., Karlsson, H. O., Fernández Galván, I. & Lindh, R. (2017). How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield of Dioxetane?. Journal of Physical Chemistry Letters, 8(16), 3790-3794
Open this publication in new window or tab >>How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield of Dioxetane?
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2017 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 16, p. 3790-3794Article in journal (Refereed) Published
Abstract [en]

Chemiluminescence is the emission of light as a result of a nonadiabatic chemical reaction. The present work is concerned with understanding the yield of chemiluminescence, in particular how it dramatically increases upon methylation of 1,2-dioxetane. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction of various methyl-substituted dioxetanes have been simulated. Methyl-substitution leads to a significant increase in the dissociation time scale. The rotation around the O-C-C-O dihedral angle is slowed; thus, the molecular system stays longer in the "entropic trap" region. A simple kinetic model is proposed to explain how this leads to a higher chemiluminescence yield. These results have important implications for the design of efficient chemiluminescent systems in medical, environmental, and industrial applications.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2017
National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-334304 (URN)10.1021/acs.jpclett.7b01668 (DOI)000408187400012 ()28749694 (PubMedID)
Funder
Swedish Research Council, 2016-03398
Available from: 2017-11-23 Created: 2017-11-23 Last updated: 2018-08-20
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7567-8295

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