Photoelectron spectra of the nucleobases cytosine, thymine and adenine

Trofimov, A. B.; Schirmer, J.; Кобычев, В. Б.; Potts, A.W.; Holland, D.M.P.; Karlsson, Leif

doi:10.1088/0953-4075/39/2/007

Cited by 146 publications

(277 citation statements)

References 53 publications

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“…Finally, as mentioned earlier, we also wrote the code implementing the formulation of the nD-ADC(3) scheme presented in ref. 16. The results we obtained in both cases agree within the expected threshold for this kind of calculations, thus representing also an independent check of the correctness of the code.…”

Section: Integral-driven Equationssupporting

confidence: 82%

“…13 It would be highly desirable, therefore, if, starting from the standard ADC, one could devise a formalism in which the ionization and affinity block are analytically decoupled from the start, so that the evaluation of the affinity block can be altogether skipped for ionization calculations. The recently developed non-Dyson ADC(3) approach 15,16,19 (nD-ADC(3)) successfully addresses exactly this question.…”

Section: The Adc(3) Schemementioning

confidence: 99%

“…In fact, as discussed by Schirmer et al, 15 the ADC equations are not unique, and they have been reported in two different formulations. 15,16 The two versions lead to the same results to within sixth-order terms and extensive numerical comparison shows that the resulting ionization energies never differ by more than 0.01 eV. 16 We have implemented in our code both sets of formulas (which are computationally essentially equivalent) but, for simplicity, we report and discuss here only the set of equations of ref.…”

Section: Nd-adc(3) Working Equationsmentioning

confidence: 99%

“…Such a method, referred to as the S(41) scheme, has indeed been proposed and shown to lead to an approximation essentially as good as the standard DEM approximation. 16 Since we are still in a phase of comparative study of the non-Dyson and Dyson approaches, we have not yet implemented the S(41) scheme in our code, so that both methods rely on an identical evaluation of the static self-energy via the same DEM code. Work to remove the DEM bottleneck will however be undertaken in the very near future.…”

Section: Integral-driven Equationsmentioning

confidence: 99%

“…Depending on the size of the molecule, the orbital basis set, and the approximation scheme used, the configuration space can become extremely large preventing the determination of the relevant eigenvalues and eigenvectors from the corresponding secular matrix with reasonable expense. It is the purpose of the present article to describe how, building on some recent significant advances in the formal development of the theory, the so-called non-Dyson scheme, 15,16 it is possible to efficiently minimize the computational burden of Green's function investigations. To this end, we have implemented and illustrate here a new computer program for the calculation of ionization spectra that (a) makes use of the non-Dyson scheme and (b) adopts a partially integral-driven approach for the handling of the two-electron integrals.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Implementation and use of a direct, partially integral‐driven non‐Dyson propagator method for molecular ionization

2008

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The Green's function ADC(3) scheme has been for many years a successful method to predict theoretically the ionization (and electron affinity) spectrum of molecules. However, a dramatic enhancement of the method's power has come only recently, with the development of an approximation method to the one-particle Green's function which does not make direct use of the Dyson equation. In the present work, we present an efficient computer implementation of this novel approach, with first comparative tests demonstrating its enormous computational advantage over the conventional approach.

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Section: Integral-driven Equationssupporting

confidence: 82%

Section: The Adc(3) Schemementioning

confidence: 99%

Section: Nd-adc(3) Working Equationsmentioning

confidence: 99%

Section: Integral-driven Equationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Implementation and use of a direct, partially integral‐driven non‐Dyson propagator method for molecular ionization

2008

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Electronic‐Excited‐State Structures and Properties of Hydrated DNA Bases and Base Pairs

Shukla¹,

Leszczyński²

2010

Hydrogen Bonding and Transfer in the Excited State

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Computational chemistry methods have been established as an attractive and reliable alternative to the costly and time-consuming experiments used to determine structures, properties and reactivities of molecular species. Although the modelling of the exact environmental conditions at the high theoretical level is still very expensive and may not be possible in several cases, computational methods are capable of providing reliable predictions in many ways, which can be useful to experimentalists and to the general scientific community [1,2]. Theoretical methods are especially attractive in areas such as the determination of excitedstate geometries of complex molecules, where experiments are not yet possible. Another example of the role of computational studies is the quantitative prediction of amino group pyramidalization of nucleic acid bases. The neutron diffraction study of adenine crystals has suggested a non-planar amino group [3]. Using the ab initio quantum chemical method, the amino groups of bases were suggested to be non-planar more than a decade ago [4,5]. However, only recently, an experimental method has verified such non-planarity in the gas phase of adenine and cytosine, using the measurement of the vibrational transition moment angles [6]. We strongly believe that theoretical and experimental methods are complementary to each other, and a judicious decision is needed for their efficient applications to determine the structures and properties of different systems.Hydrogen bonding is ubiquitous. It plays an important role in different aspects of all living organisms. Hydrogen bonds can be classified as weak, moderate and strong, depending upon their energies [7]. Hydrogen

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Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides

Liu

O’Reilly

Schwob

et al. 2023

Chemistry A European J

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Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L-and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.

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Photoelectron spectra of the nucleobases cytosine, thymine and adenine

Cited by 146 publications

References 53 publications

Implementation and use of a direct, partially integral‐driven non‐Dyson propagator method for molecular ionization

Implementation and use of a direct, partially integral‐driven non‐Dyson propagator method for molecular ionization

Electronic‐Excited‐State Structures and Properties of Hydrated DNA Bases and Base Pairs

Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides

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