| 1. |
- Holm, Anne I. S., et al.
(författare)
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Synchrotron Radiation Circular Dichroism of Various G-Guadruplex Structures
- 2010
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 93:5, s. 429-433
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Tidskriftsartikel (refereegranskat)abstract
- Here we report synchrotron radiation circular dichroism spectra of various G-quadruplexes from 179 to 350 nm, and a number of bands in the vacuum ultraviolet (VUV) are reported for the first time. For a tetramolecular parallel structure, the strongest band in the spectrum is a negative band in the VUV at 182 nm; for a bimolecular antiparallel structure with diagonal loops, a new strong positive band is found at 190 nm; for a bimolecular parallel structure with edgewise loops, a strong positive band at 189 nm is observed; and for a self-folded chair-type structure, the strongest band in the spectrum is a positive band at 187 nm. For the tetramolecular parallel structure, the CD signals at all wavelengths are dominated by contributions from quartets of G bases, and the signal strength is approximately proportional to the number of quartets. Our experiments on well-characterized G-quadruplex structures lead us to question past attributions of CD signals to helix handedness and G quartet polarity. Although differences can be observed in the VUV region for the various quadruplex types, there do not appear to be clear-cut spectral features that can be used to identify specific topological features. It is suggested that this is because a dominant positive band in the VUV seen near 190 nm in all quadruplex structures is due to intrastrand guanine guanine base stacking. However, our spectra can serve as reference spectra for the G-quadruplex structures investigated and, not least, to benchmark theoretical calculations and empirical models.
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| 2. |
- 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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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- Palmer, Michael H., et al.
(författare)
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Interpretation of the photoelectron, ultraviolet, and vacuum ultraviolet photoabsorption spectra of bromobenzene by ab initio configuration interaction and DFT computations
- 2015
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 143:16
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Tidskriftsartikel (refereegranskat)abstract
- New photoelectron, ultraviolet (UV), and vacuum UV (VUV) spectra have been obtained for bromobenzene by synchrotron study with higher sensitivity and resolution than previous work. This, together with use of ab initio calculations with both configuration interaction and time dependent density functional theoretical methods, has led to major advances in interpretation. The VUV spectrum has led to identification of a considerable number of Rydberg states for the first time. The Franck-Condon (FC) analyses including both hot and cold bands lead to identification of the vibrational structure of both ionic and electronically excited states including two Rydberg states. The UV onset has been interpreted in some detail, and an interpretation based on the super-position of FC and Herzberg-Teller contributions has been performed. In a similar way, the 6 eV absorption band which is poorly resolved is analysed in terms of the presence of two pi pi* states of (1)A(1) (higher oscillator strength) and B-1(2) (lower oscillator strength) symmetries, respectively. The detailed analysis of the vibrational structure of the 2(2)B(1) ionic state is particularly challenging, and the best interpretation is based on equation-of-motion-coupled cluster with singles and doubles computations. 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. The equilibrium structures of the 3b(1)3s and 6b(2)3s (valence shell numbering) Rydberg states have been obtained and compared with the corresponding ionic limit structures.
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