| 1. |
- Chen, Shu-Feng, et al.
(author)
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Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide : A Systematic Theoretical Study
- 2012
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:8, s. 2796-2807
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Journal article (peer-reviewed)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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| 2. |
- Farahani, Pooria, 1985-, et al.
(author)
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A Two-Scale Approach to Electron Correlation in Multiconfigurational Perturbation Theory
- 2014
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In: Journal of Computational Chemistry. - : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 35:22, s. 1609-1617
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Research review (peer-reviewed)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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| 3. |
- Farahani, Pooria, 1985-, et al.
(author)
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Revisiting the Nonadiabatic Process in 1,2-Dioxetane
- 2013
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:12, s. 5404-5411
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Journal article (peer-reviewed)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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| 4. |
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| 5. |
- Giussani, Angelo, et al.
(author)
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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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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 7:12, s. 4088-4096
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Journal article (peer-reviewed)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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| 6. |
- Giussani, Angelo, et al.
(author)
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Photoinduced Formation Mechanism of the Thymine-Thymine (6-4) Adduct
- 2013
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 1999-2004
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Journal article (peer-reviewed)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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| 7. |
- Gobbo, Joao Paulo, et al.
(author)
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On the Deactivation Mechanisms of Adenine-Thymine Base Pair
- 2012
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:13, s. 4089-4097
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Journal article (peer-reviewed)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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| 8. |
- Gonzalez-Ramirez, Israel, et al.
(author)
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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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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:8, s. 2769-2776
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Journal article (peer-reviewed)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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| 9. |
- Gonzalez-Ramirez, Israel, et al.
(author)
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On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers
- 2011
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In: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 128:4-6, s. 705-711
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Journal article (peer-reviewed)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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| 10. |
- Lindh, Roland, et al.
(author)
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Computational Photochemistry and Photophysics: the state of the art
- 2012. - 40
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In: <em>Photochemistry: Volume 40</em>. - : Royal Society of Chemistry. ; , s. 42-72-, s. 42-72
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Book chapter (other academic/artistic)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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