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| 2. |
- Kõljalg, Urmas, et al.
(författare)
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Towards a unified paradigm for sequence-based identification of fungi.
- 2013
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Ingår i: Molecular ecology. - : Wiley. - 1365-294X .- 0962-1083. ; 22:21, s. 5271-7
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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| 3. |
- Palmer, Michael H., et al.
(författare)
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A combined theoretical and experimental study of the ionic states of iodopentafluorobenzene
- 2017
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 146:8
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Tidskriftsartikel (refereegranskat)abstract
- A new synchrotron radiation photoelectron spectral (PES) study of iodopentafluorobenzene, together with a theoretical analysis of the spectrum, where Franck-Condon factors are discussed, gives detailed insight into the ionization processes, and this exposes the need for a reinvestigation of the vacuum ultraviolet spectral (VUV) assignments. We have calculated adiabatic ionization energies (AIEs) for several ionic states, using the equation-of-motion coupled cluster method for ionic states combined with multi-configuration self-consistent field calculation study. The AIE sequence is: (XB1)-B-2 < A(2)A(2) < (BB2)-B-2 < C2(2)B(1) < D(2)A(1) < E3(2)B(1). This symmetry sequence has a major impact on previous VUV spectral assignments, which now appear to be to optically forbidden states. Changes in the equilibrium structures for these ionic states are relatively small, but a significant decrease and increase in the C-I bond length relative to the X(1)A(1) structure occurs for the (XB1)-B-2 and (CB1)-B-2 states, respectively. The PES shows major vibrational overlaps between pairs of ionic states, X with A, and A with B. The result of these overlaps is the loss of vibrational structure and considerable broadening of the higher energy PES state. Although the baseline is nearly re-established between the A and B states, where the two bands are nearly separate, the B state is also broadened by the A state. Only the C ionic state, which shows the most highly developed vibrational structure, can be regarded as free from vibrational coupling to a neighbor state. The Franck-Condon analysis of the PES bands X, A, B, and C is described in detail; the apparent simplicity of some of these bands is illusory, since almost all the observed peaks arise from super-position of several calculated vibrational states. The experimental AIE of the A state, which is submerged under the X state envelope, has been determined by the subtraction of the calculated X state envelope from the observed PES spectrum. The overlap of these PES bands and the apparent closeness of the potential energy curves describing them have been investigated, using the state-averaged, complete active space self-consistent field method. We have identified two structures, one where the potential energy curves for the X and A states cross and another for the A and B states. At these two conical intersections (ConInts), there is zero-energy difference within each pair of states. Although similar in energy, the ConInt for the crossing of the X with A states, and that for the A with B states, shows that the open-shell occupancies correspond to the 4 lowest AIE states, and all four states that are quite different from each other. Published by AIP Publishing.
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| 4. |
- Palmer, Michael H., et al.
(författare)
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A combined theoretical and experimental study of the valence and Rydberg states of iodopentafluorobenzene
- 2017
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Ingår i: Journal of Chemical Physics. - : AMER INST PHYSICS. - 0021-9606 .- 1089-7690. ; 146:17
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Tidskriftsartikel (refereegranskat)abstract
- A new ultraviolet (UV) and vacuum ultraviolet (VUV) spectrum for iodopentafluorobenzene (C6F5I) using synchrotron radiation is reported. The measurements have been combined with those from a recent high-resolution photoelectron spectroscopic study. A major theoretical study, which includes both Franck-Condon (FC) and Herzberg-Teller (HT) analyses, leads to conclusions, which are compatible with both experimental studies. Our observation that the VUV multiplet at 7.926 eV in the VUV spectrum is a Rydberg state rather than a valence state leads to a fundamental reassignment of the VUV Rydberg spectrum over previous studies and removes an anomaly where some previously assigned Rydberg states were to optically forbidden states. Adiabatic excitation energies (AEEs) were determined from equations-of-motion coupled cluster with singles and doubles excitation; these were combined with time dependent density functional theoretical methods. Frequencies from these two methods are very similar, and this enabled the evaluation of both FC and HT contributions in the lower valence states. Multi-reference multi-root configuration interaction gave a satisfactory account of the principal UV+ VUV spectral profile of C6F5I, with vertical band positions and intensities. The UV spectral onset consists of two very weak transitions assigned to 1(1)B(1) (pi sigma*) and 1(1)B(2) (sigma sigma*) symmetries. The lowest unoccupied molecular orbital of a sigma*(a(1)) symmetry has a significant C-I* antibonding character. This results in considerable lengthening of the C-I bond for both these excited states. The vibrational intensity of the lowest 11B1 state is dominated by HT contributions; the 1(1)B(2) state contains both HT and FC contributions; the third band, which contains three states, two pi pi*(1(1)A(1), 2(1)B(2)) and one pi sigma*(2(1)B(1)), is dominated by FC contributions in the (1)A(1) state. In this (1)A(1) state, and the spectrally dominant bands near 6.7 ((1)A(1)) and 7.3 eV ((1)A(1) + B-1(2)), the C-I bond length is in the normal range, and FC components dominate.
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| 5. |
- Palmer, Michael H., et al.
(författare)
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Combined theoretical and experimental study of the valence, Rydberg, and ionic states of chlorobenzene
- 2016
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 144:12
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Tidskriftsartikel (refereegranskat)abstract
- New photoelectron (PE) and ultra violet (UV) and vacuum UV (VUV) spectra have been obtained for chlorobenzene by synchrotron study with higher sensitivity and resolution than previous work and are subjected to detailed analysis. In addition, we report on the mass-resolved (2 + 1) resonance enhanced multiphoton ionization (REMPI) spectra of a jet-cooled sample. Both the VUV and REMPI spectra have enabled identification of a considerable number of Rydberg states for the first time. The use of ab initio calculations, which include both multi-reference multi-root doubles and singles configuration interaction (MRD-CI) and time dependent density functional theoretical (TDDFT) methods, has led to major advances in interpretation of the vibrational structure of the ionic and electronically excited states. Franck-Condon (FC) analyses of the PE spectra, including both hot and cold bands, indicate much more complex envelopes than previously thought. The sequence of ionic states can be best interpreted by our multi-configuration self-consistent field computations and also by comparison of the calculated vibrational structure of the B and C ionic states with experiment; these conclusions suggest that the leading sequence is the same as that of iodobenzene and bromobenzene, namely: (XB1)-B-2(3b(1)(-1)) < A(2)A(2)(1a(2)(-1)) < (BB2)-B-2(6b(2)(-1)) < (CB1)-B-2(2b(1)(-1)). The absorption onset near 4.6 eV has been investigated using MRD-CI and TDDFT calculations; the principal component of this band is B-1(2) and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. The other low-lying absorption band near 5.8 eV is dominated by a (1)A(1) state, but an underlying weak B-1(1) state (pi sigma*) is also found. The strongest band in the VUV spectrum near 6.7 eV is poorly resolved and is analyzed in terms of two pi pi* states of (1)A(1) (higher oscillator strength) and B-1(2) (lower oscillator strength) symmetries, respectively. The calculated vertical excitation energies of these two states are critically dependent upon the presence of Rydberg functions in the basis set, since both manifolds are strongly perturbed by the Rydberg states in this energy range. A number of equilibrium structures of the ionic and singlet excited states show that the molecular structure is less subject to variation than corresponding studies for iodobenzene and bromobenzene.
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| 6. |
- Palmer, Michael H., et al.
(författare)
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Combined theoretical and experimental study of the valence, Rydberg and ionic states of fluorobenzene
- 2016
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 144:20
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Tidskriftsartikel (refereegranskat)abstract
- New photoelectron spectra (PES) and ultra violet (UV) and vacuum UV (VUV) absorption spectra of fluorobenzene recorded at higher resolution than previously, have been combined with mass-resolved (2 + 1) and (3 + 1) resonance enhanced multiphoton ionization (REMPI) spectra; this has led to the identification of numerous Rydberg states. The PES have been compared with earlier mass-analyzed threshold ionization and photoinduced Rydberg ionization (PIRI) spectra to give an overall picture of the ionic state sequence. The analysis of these spectra using both equations of motion with coupled cluster singles and doubles (EOM-CCSD) configuration interaction and time dependent density functional theory (TDDFT) calculations have been combined with vibrational analysis of both the hot and cold bands of the spectra, in considerable detail. The results extend several earlier studies on the vibronic coupling leading to conical intersections between the (XB1)-B-2 and A(2)A(2) states, and a further trio (B, C, and D) of states. The conical intersection of the X and A states has been explicitly identified, and its structure and energetics evaluated. The energy sequence of the last group is only acceptable to the present study if given as (BB2)-B-2 < (CB1)-B-2 < D(2)A(1), a conclusion which is in agreement with most previous EOM-CCSD and other calculations. However, this symmetry ordering of the B and C states forces reconsideration of the nature of the PIRI spectrum. The coupling between these two states is induced by the a(2) modes, v(12) and v(14) and we propose that the 14(1) band is observed in the (BB2)-B-2 band in the PES for the first time, because of the improved resolution. This same assignment is given to the lowest energy band in the PIRI spectrum which was previously assigned as the origin band and further conclude that the entire PIRI spectrum is induced by v(12) and v(14). The relative intensities of the various Rydberg state peaks in the VUV absorption and REMPI spectra of fluorobenzene are very similar to those observed in the equivalent spectra of benzene. Published by AIP Publishing.
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