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The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase
KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
CNR-INFM, Laboratorio Nazionale TASC, Trieste.
CNR-IMIP, Montelibretti, Rome.
Show others and affiliations
2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 4, 044316-1-044316-12 p.Article in journal (Refereed) Published
Abstract [en]

Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with pi* symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to transitions to valence/Rydberg orbitals with mixed pi*/sigma* character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to sigma* orbitals. Calculating the experimental and theoretical Delta(pi) term values at both edges, we observe that they are almost the same within +/- 1 eV as expected for isoelectronic bonded pairs. The term values of the pi* and sigma* resonances are discussed in terms of the total Z number of the atoms participating in the bond.

Place, publisher, year, edition, pages
2008. Vol. 128, no 4, 044316-1-044316-12 p.
Keyword [en]
Density functional theory; Ionization potential; Molecular orbitals; Resonance; Rydberg states; X ray absorption near edge structure spectroscopy; Gas phases; Pyrimidine; Rydberg orbitals
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:kth:diva-8340DOI: 10.1063/1.2822985ISI: 000252821200039Scopus ID: 2-s2.0-38849108213OAI: oai:DiVA.org:kth-8340DiVA: diva2:13634
Note
QC 20100726Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-09-16Bibliographically approved
In thesis
1. First Principles Studies of Carbon Based Molecular Materials
Open this publication in new window or tab >>First Principles Studies of Carbon Based Molecular Materials
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The aim of this thesis was to investigate carbon based molecular materials at first principles levels. Special attention has been paid to simulations of X-ray spectroscopies, including near edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron, and X-ray emission spectroscopy, which can provide detailed information about core, occupied and unoccupied molecular orbitals of the systems under investigation. Theoretical calculations have helped to assign fine spectral structures in high resolution NEXAFS spectra of five azabenzenes (pyridine, pyrazine, pyrimidine, pyridazine and s-triazine), and to identify different local chemical environments among them. With the help of NEXAFS, the characters of important chemical bonds that might be responsible for the unique magnetic properties of the tetracyanoethylene compound has been revealed. Calculations have demonstrated that X-ray spectroscopies are powerful tools for isomer identification and structure determination of fullerenes and endohedral metallofullerenes. A joint experimental and theoretical study on metallofullerene Gd@C82 has firmly determined its equilibrium structure, in which the gadolinium atom lies above the hexagon on the C2 axis. It is found that the gadolinium atom could oscillate around its equilibrium position and that its oscillation amplitude increases with increasing temperature.

In this thesis, several new computational schemes for large-scale systems have been proposed. Parallel implementation of a central insertion scheme (CIS) has been realized, which allows to effectively calculate electronic structures of very large systems, up to 150,000 electrons, at hybrid density functional theory levels. In comparison with traditional computational methods, CIS provides results with the same high accuracy but requires only a fraction of computational time. One of its applications is to calculate electronic structures of nanodiamond clusters varying from 0.76 nm (29 carbons) to 7.3 nm (20,959 carbons) in diameter, which enabled to resolve the long-standing debate about the validity of the quantum confinement model for nanodiamonds. Electronic structures and X-ray spectroscopies of a series of single-walled carbon nanotubes (SWCNTs) with different diameters and lengths have been calculated, which have made it possible to interpret the existing experimental results.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. x, 63 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:10
Keyword
first principles simulations, carbon based molecular materials, X-ray spectroscopies
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-4724 (URN)978-91-7178-963-1 (ISBN)
Public defence
2008-05-23, FB42, AlbaNova, Roslagstullsbaken 21, Stockholm, 10:00
Opponent
Supervisors
Note
QC 20100727Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-07-27Bibliographically approved
2. Synchrotron radiation studies of gas phase molecules: from hydrogen to DNA sugars
Open this publication in new window or tab >>Synchrotron radiation studies of gas phase molecules: from hydrogen to DNA sugars
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

This thesis summarises experimental results on the molecular spectroscopy of gas phase molecules excited by synchrotron radiation in the VUV and soft X-ray regions. We have used three different detection techniques, photon induced fluorescence spectroscopy, photoionisation mass spectroscopy and near edge X-ray absorption fine structure spectroscopy to study molecular deuterium, hydrogen sulphide, ammonia, methanol, pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, and 2-deoxy-D-ribose, the last one also known as the DNA sugar. Out of this variety of techniques and molecules we have shown that: (1) high resolution dispersed fluorescence allows us to identify vibrational and rotational bands in molecular deuterium, as well as to estimate the predissociation probability of the same molecule [paper I]; (2) the main species fluorescing after core excitation of methane, ammonia [paper III], hydrogen sulphide [paper II], pyridine, pyrimidine and s-triazine is H Balmer α, followed by fluorescence from ionised species, molecular bands and Balmer β, γ , δ; (3) the Rydberg enhancement seen in fluorescence measurements of water [Melero et al. PRL 96 (2006) 063003], corroborated later in H2S [paper II], NH3 [paper III] and CH4 [paper III] and postulated as general behaviour for molecules formed by low-Z atoms, is also seen in larger organic cyclic molecules, e.g. azabenzenes; (4) when dissociative ionisation of pyridine, pyridazine, pyrimidine, pyrazine, s-triazine and 2-deoxy-D-ribose occurs, concerted bond rearrangement and nuclear motion takes place as opposed to stepwise dissociation [papers V and VI].

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. x, 56 p.
Series
Trita-FYS, ISSN 0280-316X ; 2008:1
Keyword
KTH thesis, synchrotron radiation, gas phase, bio molecules
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-4640 (URN)978-91-7178-852-8 (ISBN)
Public defence
2008-03-13, FA31, Albanova, Roslagstullabacken 21, Stockholm, 10:15
Opponent
Supervisors
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved

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