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  1. Article ; Online: 3-Methylation alters excited state decay in photoionised uracil.

    Segarra-Martí, Javier / Tran, Thierry / Bearpark, Michael J

    Physical chemistry chemical physics : PCCP

    2022  Volume 24, Issue 44, Page(s) 27038–27046

    Abstract: UV and VUV-induced processes in DNA/RNA nucleobases are central to understand photo-damaging and photo-protecting mechanisms in our genetic material. Here we model the events following photoionisation and electronic excitation in uracil, methylated in ... ...

    Abstract UV and VUV-induced processes in DNA/RNA nucleobases are central to understand photo-damaging and photo-protecting mechanisms in our genetic material. Here we model the events following photoionisation and electronic excitation in uracil, methylated in the 1' and 3' positions, using the correlated XMS-CASPT2 method. We compare our results against those for uracil and 5-methyl-uracil (thymine) previously published. We find 3-methylation, an epigenetic modification in non-negligible amounts, shows the largest differences in photoionised decay of all three derivatives studied compared to uracil itself. At the S
    MeSH term(s) Uracil ; Methylation ; Thymine ; RNA
    Chemical Substances Uracil (56HH86ZVCT) ; Thymine (QR26YLT7LT) ; RNA (63231-63-0)
    Language English
    Publishing date 2022-11-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d2cp03460c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Modelling Photoionisation in Isocytosine: Potential Formation of Longer-Lived Excited State Cations in its Keto Form.

    Segarra-Martí, Javier / Bearpark, Michael J

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2021  Volume 22, Issue 21, Page(s) 2140

    Abstract: The front cover artwork is provided by Dr. Javier Segarra-Martí (University of Valencia, Spain) and Prof. Michael J. Bearpark (Imperial College London, UK). The image shows the ultrafast photoionisation of DNA canonical nucleobase cytosine and the slower ...

    Abstract The front cover artwork is provided by Dr. Javier Segarra-Martí (University of Valencia, Spain) and Prof. Michael J. Bearpark (Imperial College London, UK). The image shows the ultrafast photoionisation of DNA canonical nucleobase cytosine and the slower ionization process in non-canonical base isocytosine embedded within a DNA backbone. Read the full text of the Article at 10.1002/cphc.202100402.
    MeSH term(s) Cations/chemistry ; Cytosine/analogs & derivatives ; Cytosine/chemistry ; DNA/chemistry ; Ketones/chemistry ; Models, Molecular ; Molecular Structure ; Photochemical Processes ; Ultraviolet Rays
    Chemical Substances Cations ; Ketones ; isocytosine (108-53-2) ; Cytosine (8J337D1HZY) ; DNA (9007-49-2)
    Language English
    Publishing date 2021-11-22
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2025223-7
    ISSN 1439-7641 ; 1439-4235
    ISSN (online) 1439-7641
    ISSN 1439-4235
    DOI 10.1002/cphc.202100733
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Modelling Photoionisation in Isocytosine: Potential Formation of Longer-Lived Excited State Cations in its Keto Form.

    Segarra-Martí, Javier / Bearpark, Michael J

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2021  Volume 22, Issue 21, Page(s) 2172–2181

    Abstract: Studying the effects of UV and VUV radiation on non-canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent ... ...

    Abstract Studying the effects of UV and VUV radiation on non-canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS-CASPT2 theoretical study of the photoionisation of non-canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including
    MeSH term(s) Cations/chemistry ; Cytosine/analogs & derivatives ; Cytosine/chemistry ; Ketones/chemistry ; Models, Molecular ; Molecular Structure ; Photochemical Processes ; Ultraviolet Rays
    Chemical Substances Cations ; Ketones ; isocytosine (108-53-2) ; Cytosine (8J337D1HZY)
    Language English
    Publishing date 2021-09-07
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2025223-7
    ISSN 1439-7641 ; 1439-4235
    ISSN (online) 1439-7641
    ISSN 1439-4235
    DOI 10.1002/cphc.202100402
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Coherent Mixing of Singlet and Triplet States in Acrolein and Ketene: A Computational Strategy for Simulating the Electron-Nuclear Dynamics of Intersystem Crossing.

    Danilov, Don / Jenkins, Andrew J / Bearpark, Michael J / Worth, Graham A / Robb, Michael A

    The journal of physical chemistry letters

    2023  Volume 14, Issue 26, Page(s) 6127–6134

    Abstract: We present a theoretical study of intersystem crossing (ISC) in acrolein and ketene with the Ehrenfest method that can describe a superposition of singlet and triplet states. Our simulations illustrate a new mechanistic effect of ISC, namely, that a ... ...

    Abstract We present a theoretical study of intersystem crossing (ISC) in acrolein and ketene with the Ehrenfest method that can describe a superposition of singlet and triplet states. Our simulations illustrate a new mechanistic effect of ISC, namely, that a superposition of singlets and triplets yields nonadiabatic dynamics characteristic of that superposition rather than the constituent state potential energy surfaces. This effect is particularly significant in ketene, where mixing of singlet and triplet states along the approach to a singlet/singlet conical intersection occurs, with the spin-orbit coupling (SOC) remaining small throughout. In both cases, the effects require many recrossings of the singlet/triplet state crossing seam, consistent with the textbook treatment of ISC.
    Language English
    Publishing date 2023-06-26
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c01187
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  5. Article ; Online: How electronic superpositions drive nuclear motion following the creation of a localized hole in the glycine radical cation.

    Danilov, Don / Tran, Thierry / Bearpark, Michael J / Marangos, Jon P / Worth, Graham A / Robb, Michael A

    The Journal of chemical physics

    2022  Volume 156, Issue 24, Page(s) 244114

    Abstract: In this work, we have studied the nuclear and electron dynamics in the glycine cation starting from localized hole states using the quantum Ehrenfest method. The nuclear dynamics is controlled both by the initial gradient and by the instantaneous ... ...

    Abstract In this work, we have studied the nuclear and electron dynamics in the glycine cation starting from localized hole states using the quantum Ehrenfest method. The nuclear dynamics is controlled both by the initial gradient and by the instantaneous gradient that results from the oscillatory electron dynamics (charge migration). We have used the Fourier transform (FT) of the spin densities to identify the "normal modes" of the electron dynamics. We observe an isomorphic relationship between the electron dynamics normal modes and the nuclear dynamics, seen in the vibrational normal modes. The FT spectra obtained this way show bands that are characteristic of the energy differences between the adiabatic hole states. These bands contain individual peaks that are in one-to-one correspondence with atom pair (+·) ↔ (·+) resonances, which, in turn, stimulate nuclear motion involving the atom pair. With such understanding, we anticipate "designer" coherent superpositions that can drive nuclear motion in a particular direction.
    MeSH term(s) Cations ; Electronics ; Electrons ; Glycine ; Motion
    Chemical Substances Cations ; Glycine (TE7660XO1C)
    Language English
    Publishing date 2022-04-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0093780
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    In stock of ZB MED Bonn / Germany

    Z 4' 49/16: Show issues

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  6. Article ; Online: Ultrafast and radiationless electronic excited state decay of uracil and thymine cations: computing the effects of dynamic electron correlation.

    Segarra-Martí, Javier / Tran, Thierry / Bearpark, Michael J

    Physical chemistry chemical physics : PCCP

    2019  Volume 21, Issue 26, Page(s) 14322–14330

    Abstract: In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with ... ...

    Abstract In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with XMS-CASPT2). In both systems, we find that one state of
    Language English
    Publishing date 2019-01-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c8cp07189f
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  7. Article ; Online: Molecular excited state calculations with adaptive wavefunctions on a quantum eigensolver emulation: reducing circuit depth and separating spin states.

    Chan, Hans Hon Sang / Fitzpatrick, Nathan / Segarra-Martí, Javier / Bearpark, Michael J / Tew, David P

    Physical chemistry chemical physics : PCCP

    2021  Volume 23, Issue 46, Page(s) 26438–26450

    Abstract: ... Ab ... ...

    Abstract Ab initio
    Language English
    Publishing date 2021-12-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d1cp02227j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Molecular Vertical Excitation Energies Studied with First-Order RASSCF (RAS[1,1]): Balancing Covalent and Ionic Excited States.

    Tran, Thierry / Segarra-Martí, Javier / Bearpark, Michael J / Robb, Michael A

    The journal of physical chemistry. A

    2019  Volume 123, Issue 25, Page(s) 5223–5230

    Abstract: RASSCF calculations of vertical excitation energies were carried out on a benchmark set of 19 organic molecules studied by Thiel and co-workers [ J. Chem. Phys. 2008 , 128 , 134110 ]. The best results, in comparison with the MS-CASPT2 results of Thiel, ... ...

    Abstract RASSCF calculations of vertical excitation energies were carried out on a benchmark set of 19 organic molecules studied by Thiel and co-workers [ J. Chem. Phys. 2008 , 128 , 134110 ]. The best results, in comparison with the MS-CASPT2 results of Thiel, were obtained using a RASSCF space that contains at most one hole and one particle in the RAS1 and RAS3 spaces, respectively, which we denote as RAS[1,1]. This subset of configurations recovers mainly the effect of polarization and semi-internal electronic correlation that is only included in CASSCF in an averaged way. Adding all-external correlation by allowing double excitations from RAS1 and RAS2 into RAS3 did not improve the results, and indeed, they were slightly worse. The accuracy of the first-order RASSCF computations is demonstrated to be a function of whether the state of interest can be classified as covalent or ionic in the space of configurations built from orbitals localized onto atomic sites. For covalent states, polarization and semi-internal correlation effects are negligible (RAS[1,1]), while for ionic states, these effects are large (because of inherent diffusiveness of these states compared to the covalent states) and, thus, an acceptable agreement with MS-CASPT2 can be obtained using first-order RASSCF with the extra basis set involving 3p orbitals in most cases. However, for those ionic states that are quasi-degenerate with a Rydberg state or for nonlocal nπ* states, there remains a significant error resulting from all external correlation effects.
    Language English
    Publishing date 2019-06-13
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.9b03715
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  9. Article ; Online: Excited-State Decay in the Photoisomerisation of Azobenzene: A New Balance between Mechanisms.

    Casellas, Josep / Bearpark, Michael J / Reguero, Mar

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2016  Volume 17, Issue 19, Page(s) 3068–3079

    Abstract: The mechanism of the photoisomerisation of azobenzene has been studied by means of multiconfigurational ab initio calculations. Our results show that it is necessary to account for the dynamic electron correlation in the location of the critical points ( ... ...

    Abstract The mechanism of the photoisomerisation of azobenzene has been studied by means of multiconfigurational ab initio calculations. Our results show that it is necessary to account for the dynamic electron correlation in the location of the critical points (CASPT2 optimizations) to obtain a correct description of the topography of the potential energy surfaces of the low energy singlet excited states. By using this methodology, we have found that the state populated by the initial excitation is the S
    Language English
    Publishing date 2016-10-05
    Publishing country Germany
    Document type Journal Article
    ISSN 1439-7641
    ISSN (online) 1439-7641
    DOI 10.1002/cphc.201600502
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  10. Article ; Online: Electron Dynamics upon Ionization of Polyatomic Molecules: Coupling to Quantum Nuclear Motion and Decoherence.

    Vacher, Morgane / Bearpark, Michael J / Robb, Michael A / Malhado, João Pedro

    Physical review letters

    2017  Volume 118, Issue 8, Page(s) 83001

    Abstract: Knowledge about the electronic motion in molecules is essential for our understanding of chemical reactions and biological processes. The advent of attosecond techniques opens up the possibility to induce electronic motion, observe it in real time, and ... ...

    Abstract Knowledge about the electronic motion in molecules is essential for our understanding of chemical reactions and biological processes. The advent of attosecond techniques opens up the possibility to induce electronic motion, observe it in real time, and potentially steer it. A fundamental question remains the factors influencing electronic decoherence and the role played by nuclear motion in this process. Here, we simulate the dynamics upon ionization of the polyatomic molecules paraxylene and modified bismethylene-adamantane, with a quantum mechanical treatment of both electron and nuclear dynamics using the direct dynamics variational multiconfigurational Gaussian method. Our simulations give new important physical insights about the expected decoherence process. We have shown that the decoherence of electron dynamics happens on the time scale of a few femtoseconds, with the interplay of different mechanisms: the dephasing is responsible for the fast decoherence while the nuclear overlap decay may actually help maintain it and is responsible for small revivals.
    Language English
    Publishing date 2017-02-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.118.083001
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    In stock of ZB MED Bonn / Germany

    Z 4' 58/153: Show issues

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