| 1. |
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| 2. |
- Giussani, Angelo, et al.
(författare)
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Molecular Basis of the Chemiluminescence Mechanism of Luminol
- 2019
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Ingår i: Chemistry - A European Journal. - : WILEY-V C H VERLAG GMBH. - 0947-6539 .- 1521-3765. ; 25:20, s. 5202-5213
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Tidskriftsartikel (refereegranskat)abstract
- Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.
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| 3. |
- Manni, Giovanni Li, et al.
(författare)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Tidskriftsartikel (refereegranskat)abstract
- The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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| 4. |
- Augusto, Felipe A., et al.
(författare)
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Mechanism of activated chemiluminescence of cyclic peroxides : 1,2-dioxetanes and 1,2-dioxetanones
- 2017
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 19:5, s. 3955-3962
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Chen, Shu-Feng, et al.
(författare)
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Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide : A Systematic Theoretical Study
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:8, s. 2796-2807
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- El-Zohry, Ahmed M., et al.
(författare)
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Ultrafast Twisting of the Indoline Donor Unit Utilized in Solar Cell Dyes : Experimental and Theoretical Studies
- 2015
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:5, s. 2249-2259
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Tidskriftsartikel (refereegranskat)abstract
- Previous time-resolved measurements on D149, the most-studied dye of the indoline family, had shown a fast time-component of 20–40 ps that had tentatively been attributed to structural relaxation. Using femtosecond transient absorption, we have investigated the isolated indoline donor unit (i.e., without acceptor group) and found an ultrafast decay characterized by two lifetimes of 3.5 and 23 ps. Density functional theory calculations show π-bonding and π*-antibonding character of the central ethylene group for the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO), respectively. The LUMO is localized on the flexible vinyl-diphenyl region of the donor unit and a twisting process is assumed to occur as a deactivation process for the excited molecule. This is confirmed by multireference second-order perturbation theory (CASSCF/CASPT2) calculations of the lowest-lying excited state, in which it is shown that torsion of the ethylene bond to 96° and pyramidalization to ca. 100° lead to a conical intersection with the ground state. Embedded in a plastic matrix, where double bond rotation is hindered, the decay is slowed down to nanoseconds. We have also investigated the dyes D102, D131, and D149, possessing the same indoline donor unit, by femtosecond transient absorption and found a similar decay component. The ca. 20 ps deactivation channel in D-family dyes is thus attributed to a twisting process of the donor unit. The fluorescence quantum yields of this unit and D149 were measured, and from comparison, the competition of the discovered twisting deactivation channel to the radiative decay of the excited indoline dyes could be confirmed. Blocking this deactivation channel is expected to further increase efficiency for the indoline dyes.
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| 7. |
- Farahani, Pooria, 1985-, et al.
(författare)
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A Two-Scale Approach to Electron Correlation in Multiconfigurational Perturbation Theory
- 2014
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Ingår i: Journal of Computational Chemistry. - : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 35:22, s. 1609-1617
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Forskningsöversikt (refereegranskat)abstract
- We present a new approach for the calculation of dynamicelectron correlation effects in large molecular systems usingmulticonfigurational second-order perturbation theory(CASPT2). The method is restricted to cases where partitioningof the molecular system into an active site and an environment is meaningful. Only dynamic correlation effects derivedfrom orbitals extending over the active site are included at theCASPT2 level of theory, whereas the correlation effects of theenvironment are retrieved at lower computational costs. Forsufficiently large systems, the small errors introduced by thisapproximation are contrasted by the substantial savings inboth storage and computational demands compared to thefull CASPT2 calculation. Provided that static correlation effectsare correctly taken into account for the whole system, the proposed scheme represent a hierarchical approach to the electron correlation problem, where two molecular scales aretreated each by means of the most suitable level of theory.
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| 8. |
- Farahani, Pooria, 1985-, et al.
(författare)
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Advances in computationalphotochemistry and chemiluminescenceof biological and nanotechnologicalmolecules
- 2017. - 44
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Ingår i: Photochemistry. - Cambridge, UK : Royal Society of Chemistry. - 1465-1947. ; , s. 16-60, s. 16-60
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Bokkapitel (refereegranskat)abstract
- Recent advances (2014–2015) in computational photochemistry and chemiluminescencederive from the development of theory and from the application of state-of-the-art andnew methodology to challenging electronic-structure problems. Method developmentshave mainly focused, first, on the improvement of approximate and cheap methods toprovide a better description of non-adiabatic processes, second, on the modification ofaccurate methods in order to decrease the computation time and, finally, on dynamicsapproaches able to provide information that can be directly compared with experimentaldata, such as yields and lifetimes. Applications of the ab initio quantum-chemistry methodshave given rise to relevant findings in distinct fields of the excited-state chemistry.We brieflysummarise, in this chapter, the achievements on photochemical mechanisms andchemically-induced excited-state phenomena of interest in biology and nanotechnology.
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| 9. |
- Farahani, Pooria, 1985-, et al.
(författare)
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Revisiting the Nonadiabatic Process in 1,2-Dioxetane
- 2013
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:12, s. 5404-5411
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Tidskriftsartikel (refereegranskat)abstract
- Determining the ground and excited-statedecomposition mechanisms of 1,2-dioxetane is essential tounderstand the chemiluminescence and bioluminescencephenomena. Several experimental and theoretical studies hasbeen 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′ andC−C′ bond dissociations. New high-level multistate multiconfigurational 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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| 10. |
- Farahani, Pooria, 1985-, et al.
(författare)
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Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane
- 2015
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 17, s. 18653-18664
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 11. |
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| 12. |
- Francés-Monerris, Antonio, et al.
(författare)
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Triplet versus singlet chemiexcitation mechanism in dioxetanone : a CASSCF/CASPT2 study
- 2017
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 136:6
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Tidskriftsartikel (refereegranskat)abstract
- Chemiluminescence is a fundamental process of chemistry consisting in the conversion of chemical energy stored in chemical bonds into light. It is used by nature and by man-made technology, being especially relevant in chemical analysis. The understanding of the phenomenon strongly relies in the study of peroxide models such as 1,2-dioxetanones. In the present contribution, the singlet S2 and the triplet T2 potential energy surfaces of the unimolecular decomposition of 1,2-dioxetanone have been mapped along the O-O and C-C bond coordinates on the grounds of the multiconfigurational CASPT2//CASSCF approach. Results confirm the energy degeneracy between T2, T1, S1, and S0 at the TS region, whereas S2 is unambiguously predicted at higher energies. Triplet-state population is also supported by the spin-orbit couplings between the singlet and triplet states partaking in the process. In particular, the first-principle calculations show that decomposition along the T2 state is a competitive process, having a small (similar to 3 kcal/mol) energy barrier from the ground-state TS structure. The present findings can explain the higher quantum yield of triplet-state population with respect to the excited singlet states recorded experimentally for the uni-molecular decomposition of 1,2-dioxetanone models.
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| 13. |
- Giussani, Angelo, et al.
(författare)
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Essential on the Photophysics and Photochemistry of the lndole Chromophore by Using a Totally Unconstrained Theoretical Approach
- 2011
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 7:12, s. 4088-4096
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Tidskriftsartikel (refereegranskat)abstract
- Indole is a chromophore present in many different molecules of biological interest, such as the essential amino acid tryptophan and the neurotransmitter serotonin. On the basis of CASPT2//CASSCF quantum chemical calculations, the photophysical properties of the system after UV irradiation have been studied through the exploration of the potential energy hypersurfaces of the singlet and triplet low-lying valence excited states. In contrast to previous studies, the present work has been carried out without imposing any restriction to the geometry of the molecule (C(1) symmetry) and by performing minimum energy path calculations, which is the only instrument able to provide the lowest-energy evolution of the system. Relevant findings to the photophysics of bare indole have been obtained, which compete with the currently accepted mechanism for the energy decay in the molecule. The results show the presence of a conical intersection (CI) between the initially populated (1)(L(a) pi pi*) and the (1)(L(b) pi pi*) state, easily accessible through a barrierless pathway from the Franck Condon region. At this CI region, part of the population is switched from the bright (1)(L(a) pi pi*) state to the (1)(L(b) pi pi*) state, and the system evolves toward a minimum structure from which the expected fluorescence takes place. The reported low values of the fluorescence quantum yield are explained by means of a new nonracliative mechanism specific for the (1)(L(b) pi pi*) state, in which the presence of an ethene-like CI between the (1)(L(b) pi pi*) and ground states is the main feature.
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| 14. |
- Giussani, Angelo, et al.
(författare)
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Photoinduced Formation Mechanism of the Thymine-Thymine (6-4) Adduct
- 2013
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 1999-2004
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Tidskriftsartikel (refereegranskat)abstract
- The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet 3(n pi*) state of thymine. This state, displaying an elongated C-4=O bond, triggers (6-4) dimer formation by reaction with the C-5=C-6 double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just one thymine, whose main decay channel (by radiationless repopulation of its ground state) is nonphotochemical, can rationalize the experimentally observed low quantum yield of formation for the thymine-thymine (6-4) adduct.
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| 15. |
- Gobbo, Joao Paulo, et al.
(författare)
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On the Deactivation Mechanisms of Adenine-Thymine Base Pair
- 2012
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:13, s. 4089-4097
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Tidskriftsartikel (refereegranskat)abstract
- In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)] and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.
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| 16. |
- Gonzalez-Ramirez, Israel, et al.
(författare)
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On the N-1-H and N-3-H Bond Dissociation in Uracil by Low Energy Electrons : A CASSCF/CASPT2 Study
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:8, s. 2769-2776
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Tidskriftsartikel (refereegranskat)abstract
- The dissociative electron-attachment (DEA) phenomena at the N-1-H and N-3-H bonds observed experimentally at low energies (<3 eV) in uracil are studied with the CASSCF/CASPT2 methodology. Two valence bound pi(-) and two dissociative sigma(-) states of the uracil anionic species, together with the ground state of the neutral molecule, are proven to contribute to the shapes appearing in the experimental DEA cross sections. Conical intersections (CI) between the pi(-) and sigma(-) are established as the structures which activate the DEA processes. The N-1-H and N-3-H DEA mechanisms in uracil are described, and experimental observations are interpreted on the basis of two factors: (1) the relative energy of the (U-H)(-) + H fragments obtained after DEA with respect to the ground-state equilibrium structure (S-0) of the neutral molecule (threshold for DEA) and (2) the relative energy of the CIs also with respect to S-0 (band maxima). The pi(-)(1) state is found to be mainly responsible for the N-1-H bond breaking, whereas the pi(-)(2) state is proved to be involved in the cleavage of the N-3-H bond.
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| 17. |
- Gonzalez-Ramirez, Israel, et al.
(författare)
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On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers
- 2011
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 128:4-6, s. 705-711
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Tidskriftsartikel (refereegranskat)abstract
- The UV photoreactivity of different pyrimidine DNA/RNA nucleobases along the singlet manifold leading to the formation of cyclobutane pyrimidine dimers has been studied by using the CASPT2 level of theory. The initially irradiated singlet state promotes the formation of excimers between pairs of properly oriented nucleobases through the overlap between the pi structures of two stacked nucleobases. The system evolves then to the formation of cyclobutane pyrimidine dimers via a shearing-type conical intersection activating a [2 + 2] photocycloaddition mechanism. The relative location of stable excimer conformations or alternative decay channels with respect to the reactive degeneracy region explains the differences in the photoproduction efficiency observed in the experiments for different nucleobases sequences. A comparative analysis of the main structural parameters and energetic profiles in the singlet manifold is carried out for thymine, uracil, cytosine, and 5-methylcytosine homodimers. Thymine and uracil dimers display the most favorable paths, in contrast to cytosine. Methylation of the nucleobases seems to increase the probability for dimerization.
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| 18. |
- Lindh, Roland, et al.
(författare)
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Computational Photochemistry and Photophysics: the state of the art
- 2012. - 40
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Ingår i: <em>Photochemistry: Volume 40</em>. - : Royal Society of Chemistry. ; , s. 42-72-, s. 42-72
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This review starts with the most basic concepts in photochemistry and photophysics, followed by a chronological introduction of theoretical methods and relevant applications in the history of computational photochemistry, along with the authors’ comments on the methodologies currently available for photochemical studies. Recent advances in the field are next summarized and discussed, focusing separately on methodology and computational techniques and some highlighted applied works carried out during the last two years on the topics of photodissociations, photostability, photodimerizations, photoisomerizations, proton/hydrogen transfer, photodecarboxylations, charge transport, bioexcimers, chemiluminescence and bioluminescence. We finish this review by conclusions and an outlook of the future.
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| 19. |
- Lindh, Roland, et al.
(författare)
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Non-adiabatic process in 1,2-dioxetane
- 2014
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Ingår i: Abstracts of Papers of the American Chemical Society. - 0065-7727. ; 247
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 20. |
- Lindh, Roland, 1958-, et al.
(författare)
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Recent method developments and applications in computational photochemistry, chemiluminescene and bioluminescence
- 2015. - 42
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Ingår i: <em>Photochemistry: Volume 42</em>. - Cambridge : Royal Society of Chemistry. - 9781849739566 - 9781782624547 - 9781782623038 ; , s. 11-42
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This review summarises and discusses the advances of computational photochemistry in 2012 and 2013 in both methodology and applications fields. The methodological developments of models and tools used to study and simulate non-adiabatic processes are highlighted. These developments can be summarised as assessment studies, new methods to locate conical intersections, tools for representation, interpretation and visualisation, new computational approaches and studies introducing simpler models to rationalise the quantum dynamics near and in the conical intersection. The applied works on the topics of photodissociation, photostability, photoisomerisations, proton/charge transfer, chemiluminescence and bioluminescence are summarised, and some illustrative examples of studies are analysed in more detail, particularly with reference to photostability and chemi/bioluminescence. In addition, theoretical studies analysing solvent effects are also considered. We finish this review with conclusions and an outlook on the future.
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| 21. |
- Marazzi, Marco, et al.
(författare)
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Benzophenone Ultrafast Triplet Population : Revisiting the Kinetic Model by Surface-Hopping Dynamics
- 2016
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 7:4, s. 622-626
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Tidskriftsartikel (refereegranskat)abstract
- The photochemistry of benzophenone, a paradigmatic organic molecule for photosensitization, was investigated by means of surface-hopping ab initio molecular dynamics. Different mechanisms were found to be relevant within the first 600 fs after excitation; the long debated direct (S-1 -> T-1) and indirect (S-1 -> T-2 -> T-1) mechanisms for population of the low-lying triplet state are both possible, with the latter being prevalent. Moreover, we established the existence of a kinetic equilibrium between the two triplet states, never observed before. This fact implies that a significant fraction of the overall population resides in T-2, eventually allowing one to revisit the usual spectroscopic assignment proposed by transient absorption spectroscopy. This finding is of particular interest for photocatalysis as well as for DNA damages studies because both T-1 and T-2 channels are, in principle, available for benzophenone-mediated photoinduced energy transfer toward DNA.
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| 22. |
- Navizet, Isabelle, et al.
(författare)
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Are the Bio- and Chemiluminescence States of the Firefly Oxyluciferin the Same as the Fluorescence State?
- 2013
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Ingår i: Photochemistry and Photobiology. - : Wiley. - 0031-8655 .- 1751-1097. ; 89:2, s. 319-325
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Tidskriftsartikel (refereegranskat)abstract
- A usual strategy in both experimental and theoretical studies on bio- and chemiluminescence is to analyze the fluorescent properties of the bio- and chemiluminescence reaction product. Recent findings in a coelenteramide and Cypridina oxyluciferin model arise a concern on the validity of this procedure, showing that the light emitters in each of these luminescent processes might differ. Here, the thermal decomposition path of the firefly dioxetanone and the light emission states of the Firefly oxyluciferin responsible for the bio-, chemiluminescence, and fluorescence of the molecule are characterized using ab initio quantum chemistry and hybrid quantum chemistry/molecular mechanics methods to determine if the scenario found in the coelenteramide and Cypridina oxyluciferin study does also apply to the Firefly bioluminescent systems. The results point out to a unique emission state in the bio-, chemiluminescence, and fluorescence phenomena of the Firefly oxyluciferin and, therefore, using fluorescence properties of this system is reasonable.
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| 23. |
- Navizet, Isabelle, et al.
(författare)
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The Chemistry of Bioluminescence : An Analysis of Chemical Functionalities
- 2011
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Ingår i: ChemPhysChem. - : Wiley. - 1439-4235 .- 1439-7641. ; 12:17, s. 3064-3076
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Forskningsöversikt (refereegranskat)abstract
- Firefly luciferase is one of the most studied bioluminescent systems, both theoretically and experimentally. Herein we review the current understanding of the bioluminescent process from a chemical functionality perspective based on those investigations. Three key components are emphasized: the chemiluminophore, the electron-donating fragment, and how these are affected by the substrateenzyme interaction. The understanding is based on details of how the peroxide ?O?O? bond supports the production of electronically excited products and how the charge-transfer (CT) mechanism, with the aid of an electron-donating group, lowers the activation barrier to support a reaction occurs in living organisms. For the substrateenzyme complex it is demonstrated that the enzyme can affect the hydrogen-bonding around the CT-controlling group, resulting in a mechanism for color modulation. Finally, we analyse other luciferinluciferase systems and compare them to the key chemical functionalities of the fragments of the luciferinluciferase complex with respect to similarities and differences.
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| 24. |
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| 25. |
- Roca-Sanjuán, Daniel, et al.
(författare)
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A Theoretical Analysis of the Intrinsic Light-Harvesting Properties of Xanthopterin
- 2014
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Ingår i: Computational and Theoretical Chemistry. - Netherlands : Elsevier. - 2210-271X .- 2210-2728. ; 1040-1041, s. 230-236
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Tidskriftsartikel (refereegranskat)abstract
- Belonging to the family of pterins, which are common chromophores in several bio-organisms, xanthopterin has been shown experimentally (Plotkin et al., 2010) to have the ability of acting as a light-harvesting molecule. In the present study, multiconfigurational second-order perturbation theory is used to determine the stability of distinct amino/imino and lactam/lactim tautomers and the absorption and emission spectroscopic characteristics, electron donor and acceptor properties and the electron and charge transfer efficiencies via π-stacking. The lactam–lactam form 3H5H (and in a lesser extent 1H5H) is predicted to have the most appropriate intrinsic characteristics for the light-harvesting properties of xanthopterin, since it is the most stable isomer predicted for the gas phase and estimated for polar environments, absorbs solar light at longer wave lengths, has relatively low donor properties and the presence of the keto groups, instead of enol, increases the efficiency for energy transfer through excimer-like interactions.
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| 26. |
- Roca-Sanjuán, Daniel, et al.
(författare)
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Chemiluminescence and Fluorescence States of a Small Model for Coelenteramide and Cypridina Oxyluciferin : A CASSCF/CASPT2 Study
- 2011
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 7:12, s. 4060-4069
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Tidskriftsartikel (refereegranskat)abstract
- Fluorescence and chemiluminescence phenomena are often confused in experimental and theoretical studies on the luminescent properties of chemical systems. To establish the patterns that distinguish both processes, the fluorescent and chemiluminescent states of 2-acetamido-3-methylpyrazine, which is a small model of the coelenterazine/coelenteramide and Cypridina luciferin/oxyluciferin bioluminescent systems, were characterized by using the complete active space second-order perturbation (CASPT2) method. Differences in geometries and electronic structures among the states responsible for light emission were found. On the basis of the findings, some recommendations for experimental studies on chemiluminescence are suggested, and more appropriate theoretical approaches are proposed.
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| 27. |
- Roca-Sanjuan, Daniel, et al.
(författare)
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Comment on "€œDensity functional theory study of 1,2-€dioxetanone decomposition in condensed phase€"
- 2012
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 33:26, s. 2124-2126
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Tidskriftsartikel (refereegranskat)abstract
- In the preceding paper results are presented, which are in serious conflict with state-of-the-art ab initio method. Based on these new results the authors propose a new explanation of the reason for the preferential production of a phosphorescent state. Here we show that these controversial results are flawed, since the model use exclude biradical electron structures.
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| 28. |
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| 29. |
- Roca-Sanjuan, Daniel, et al.
(författare)
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Multiconfiguration second-order perturbation theory approach to strong electron correlation in chemistry and photochemistry
- 2012
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 2:4, s. 585-603
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Forskningsöversikt (refereegranskat)abstract
- Rooted in the very fundamental aspects of many chemical phenomena, and for the majority of photochemistry, is the onset of strongly interacting electronic configurations. To describe this challenging regime of strong electron correlation, an extraordinary effort has been put forward by a young generation of scientists in the development of theories 'beyond' standard wave function and density functional models. Despite their encouraging results, a twenty-and-more-year old approach still stands as the gold standard for these problems: multiconfiguration second-order perturbation theory based on complete active space reference wave function (CASSCF/CASPT2). We will present here a brief overview of the CASSCF/CASPT2 computational protocol, and of its role in our understanding of chemical and photochemical processes.
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| 30. |
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| 31. |
- Sauri, Vicenta, et al.
(författare)
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Proton/Hydrogen Transfer Mechanisms in the Guanine-€“Cytosine Base Pair : Photostability and Tautomerism
- 2013
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:1, s. 481-496
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Tidskriftsartikel (refereegranskat)abstract
- Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine–cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contribution to tautomerism is provided. The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson–Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. In addition, the C-based imino-enol GC tautomer is thermally less stable. A study of the GC base pair is carried out subsequently taking into account the DNA surroundings in the biological environment. The most important stationary points are computed using the quantum mechanics/molecular mechanics (QM/MM) approach, suggesting a similar scenario for the proton/hydrogen-transfer phenomena in vacuo and in DNA. Finally, the static model is complemented by ab initio dynamic simulations, which show that vibrations at the hydrogen bonds can indeed originate hydrogen-transfer processes in the GC base pair. The relevance of the present findings for the rationalization of the preservation of the genetic code and mutagenesis is discussed.
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| 32. |
- Schapiro, Igor, et al.
(författare)
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A surface hopping algorithm for nonadiabatic minimum energy path calculations
- 2015
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 36:5, s. 312-20
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Tidskriftsartikel (refereegranskat)abstract
- The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base.
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| 33. |
- Schramm, Stefan, et al.
(författare)
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Investigations on the synthesis and chemiluminescence of novel 2-coumaranones
- 2013
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Ingår i: ARKIVOC. - 1551-7004 .- 1551-7012. ; :3, s. 174-188
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Tidskriftsartikel (refereegranskat)abstract
- Optimized syntheses of 2-coumaranone derivatives and, based thereon, several new representatives of this class of substances are described. They show a clearly visible chemiluminescence under the exposure of a strong base and in the presence of oxygen. The wavelength and intensity of the light emitted depends on both the substituents on the benzo annealed, as well as on the type of base used. A mechanism is presented in which a delocalized enolate is postulated as a key intermediate.
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| 34. |
- Schramm, Stefan, et al.
(författare)
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Investigations on the synthesis and chemiluminescence of novel 2-coumaranones - II
- 2015
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Ingår i: ARKIVOC. - : ARKAT USA, Inc.. - 1551-7004 .- 1551-7012. ; , s. 44-59
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Tidskriftsartikel (refereegranskat)abstract
- The optimized one-pot synthesis of 16 new 2-coumaranones containing a carbamate side-chain is described. Furthermore, the quantum yields for the base-activated chemiluminescence in the presence of oxygen was determined for all compounds, with a maximum of 5.9 +/- 0.1 x 10(-2) E mol(-1), and the application of these compounds as substitutes for usual bioluminescent and chemiluminescent reagents in bioassays is anticipated. A preliminary mechanistic pathway is also suggested, making use of recent developments regarding aspects of organic chemiluminescence, in agreement with both experimental and theoretical data available on the induced 1,2-dioxetanone decomposition as well as with the high efficiency of this reaction.
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| 35. |
- Segarra-Marti, Javier, et al.
(författare)
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Ab initio determination of the ionization potentials of water clusters (H2O)n (n=2-6)
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 136:24, s. 244306-
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Tidskriftsartikel (refereegranskat)abstract
- High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic ionization potentials of several water clusters: dimer, trimer, tetramer, pentamer, hexamer book, hexamer ring, hexamer cage, and hexamer prism. The present results establish reference values at a level not reported before for these systems, calibrating different computational strategies and helping to discard less reliable theoretical and experimental data. The systematic study with the increasing size of the water cluster allows obtaining some clues on the structure and reductive properties of liquid water.
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| 36. |
- Segarra-Marti, Javier, et al.
(författare)
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On the photophysics and photochemistry of the water dimer
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 137:24, s. 244309-
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Tidskriftsartikel (refereegranskat)abstract
- The photochemistry of the water dimer irradiated by UV light is studied by means of the complete active space perturbation theory//complete active space self-consistent field (CASPT2//CASSCF) method and accurate computational approaches like as minimum energy paths. Both electronic structure computations and ab initio molecular dynamics simulations are carried out. The results obtained show small shifts relative to a single water molecule on the vertical excitation energies of the dimer due to the hydrogen bond placed between the water donor (W-D) and the water acceptor (W-A). A red-shift and a blue-shift are predicted for the W-D and W-A, respectively, supporting previous theoretical and experimental results. The photoinduced chemistry of the water dimer is described as a process occurring between two single water molecules in which the effect of the hydrogen bond plays a minor role. Thus, the photoinduced decay routes correspond to two photodissociation processes, one for each water molecule. The proposed mechanism for the decay channels of the lowest-lying excited states of the system is established as the photochemical production of a hydrogen-bonded H2O center dot center dot center dot HO species plus a hydrogen H atom.
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| 37. |
- Vacher, Morgane, et al.
(författare)
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Chemi- and Bioluminescence of Cyclic Peroxides
- 2018
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Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 118:15, s. 6927-6974
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Forskningsöversikt (refereegranskat)abstract
- Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.
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| 38. |
- Yue, Ling, et al.
(författare)
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Can the Closed-Shell DFT Methods Describe the Thermolysis of 1,2-Dioxetanone?
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:11, s. 4359-4363
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Tidskriftsartikel (refereegranskat)abstract
- The chemiluminescent decomposition of 1,2-dioxetanone has in the past been studied by state-of-the-art multireference quantum chemical calculations, and a stepwise biradical mechanism was established. Recently, this decomposition has been reinvestigated, and a concerted mechanism has been proposed based on calculations performed at the closed-shell density functional theory (DFT) level of theory. In order to solve this apparent mechanistic contradiction, the present paper presents restricted and unrestricted DFT results obtained using functionals including different amounts of Hartree–Fock (HF) exchange, repeating and complementing the above-mentioned DFT calculations. The calculated results clearly indicate that the closed-shell DFT methods cannot correctly describe the thermolysis of 1,2-dioxetanone. It is found that unrestricted Kohn–Sham reaction energies and barriers are always lower than the ones obtained using a restricted formalism. Hence, from energy principles, the biradical mechanism is found to be prevailing in the understanding of the 1,2-dioxetanone thermolysis.
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