| 1. |
- Albinsson, Bo, 1963, et al.
(author)
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Anti, ortho, and gauche conformers of perfluoro-n-butane: Matrix-isolation IR spectra and calculations
- 1996
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In: Journal of Physical Chemistry. - 0022-3654. ; 100:9, s. 3418-3429
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Journal article (peer-reviewed)abstract
- Nitrogen matrix-isolation IR spectra have been obtained for each of the three conformers of n-C4F10 (gauche, ortho, and anti) by trapping a hot conformer mixture on a cold CsI window and subsequent matrix annealing and spectral differencing. They were assigned by comparison with results of HF/6-31G* calculations, and the nature of the normal modes has been analyzed using the total energy distribution procedure. At the fully optimized MP2/6-31G* (frozen core) level, the CCCC dihedral angles and relative energies (kcal/mol) are 54.2 degrees and 0.68 (gauche), 94.8 degrees and 1.63 (ortho), and 165.5 degrees and 0 (anti). Single-point MP2/6-311G* (frozen core) relative energies at these geometries are 0.85, 2.12, and 0 kcal/mol, respectively. Only a minute amount of the ortho conformer is trapped in nitrogen matrix, and none in other matrices that were tried. A variation of the relative intensities of IR peaks of the gauche and anti conformers as a function of the temperature of the gas before deposition yields an ''average'' Delta H value of about 0.9 kcal/mol, with the anti conformer more stable. The temperature range covered was too small to reveal the expected bilinear nature of the van't Hoff plot.
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| 2. |
- Albinsson, Bo, 1963, et al.
(author)
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Conformers of n-Si5Me12: A comparison of ab initio and molecular mechanics methods
- 1999
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In: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 103:14, s. 2184-2196
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Journal article (peer-reviewed)abstract
- Optimized geometries of the conformers of permethylated linear pentasilane, n-Si5Me12, were calculated by the HF/3-21G*, MM3, MM2, and MM+ methods, which predict eight, nine, six, and six energetically distinct enantiomeric conformer pairs, respectively, at geometries representing various combinations of the anti (similar to 165 degrees), ortho (similar to 90 degrees), and gauche (similar to 55 degrees) SiSiSiSi dihedral angles in the backbone. The results of the MM2 and MM+ methods, based on the same force field, differ insignificantly. The barriers between conformers appear to be exaggerated by the molecular mechanics methods, particularly MM2. Contour maps showing the groundstate energy as a function of the full range of two backbone SiSiSiSi dihedral angles, with all other geometrical variables optimized, computed by each of the methods (only a limited range of angles near the anti,anti geometry in the case of HF/3-21G*) are compared with each other and with analogous results for a model compound, Si4Me10. Conformer interconversion paths are discussed, and two meso transition states for enantiomer interconversion have been located at the HF/3-21G* level of calculation. At the eight HF/3-21G* optimized geometries, single-point energies (HF/6-31G* and MP2/6-31G*) and vibrational frequencies (HF/3-21G*) were computed. The predicted IR and Raman spectra suggest that about half of the expected conformers will be identifiable by vibrational spectroscopy under conditions of matrix isolation. Relative conformer energies calculated by the MM2 and HF methods are similar and favor the anti dihedral angles over gauche and ortho, in agreement with results of solution experiments. Those calculated by the hIM3 and HF methods are similar to each other and favor both anti and gauche dihedral angles nearly equally over ortho, in agreement with indications provided by gas-phase experiments. A rationalization of these solvent effects is proposed. The energies of the conformers of Si4Me10 and Si3Me12 were used to set up a system of additive increments at the MM2, MM3, HF/3-21G*, HF/6-31G*, and MP2/6-31G* levels of calculation, which can be used to predict conformational energies of longer permethylated oligosilanes. An intrinsic energy value is assigned to each of the a, o, and g dihedral angles, and interaction energy values are assigned to each combination of two dihedral angles. The interaction values follow the expected rules in that equal twist sense is favored for adjacent aa, ag, oo, and gg pairs, whereas opposite twist sense is generally favored for adjacent so and go pairs. The MM3-derived set of increments has been tested against results computed for Si6Me14 and found to perform well.
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| 3. |
- Albinsson, Bo, 1963, et al.
(author)
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Conformers of saturated chains: Matrix isolation, structure, IR and UV spectra of n-Si(4)Me(10)
- 1996
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In: Chemistry - A European Journal. - 1521-3765 .- 0947-6539. ; 2:5, s. 529-538
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Journal article (peer-reviewed)abstract
- Infrared and ultraviolet spectra of the gauche and anti conformers of matrix-isolated permethyl-n-tetrasilane have been obtained separately by taking advantage of thermally induced gauche-to-anti conversion and of wavelength-selective photochemical destruction of either conformer. The resolved UV spectrum of the gauche conformer provides the first piece of experimental evidence in favor of the recently proposed reinterpretation of conformational effects on tetrasilane electronic states. According to this, it is not the energy but the intensity of the lowest singlet excitation that changes dramatically as the SiSiSiSi dihedral angle is varied, as a result of an avoided crossing between sigma sigma* and sigma pi* states. Implications for the general understanding of sigma conjugation in simple terms are discussed. Unconstrained MP2/6-31G* optimization predicts the existence of a third backbone conformer (ortho), with a dihedral angle of about 90 degrees. Its predicted (HF/3-21G*) mid-IR spectrum is indistinguishable from that of the gauche conformer, and the matrix-isolation spectra thus provide no evidence for or against its presence.
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| 4. |
- Albinsson, Bo, 1963
(author)
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Dual fluorescence from N-6,N-6-dimethyladenosine
- 1997
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In: Journal of the American Chemical Society. - 1520-5126 .- 0002-7863. ; 119:27, s. 6369-6375
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Journal article (peer-reviewed)abstract
- The adenosine derivative N-6,N-6-dimethyladenosine (DMA) shows dual fluorescence in solvents of different polarity. In addition to the ''normal'' fluorescence at 330 nm, another band is observed at 500 nm. The long wavelength emission dominates in aprotic solvents but is dynamically quenched by protic solvents. Steady-state and lifetime measurements show that the emissions originate from two excited state species; the short wavelength emission is from the directly populated excited state which irreversibly isomerizes into the species responsible for the long wavelength emission. It is conceivable to assign the long wavelength emitting species to a twisted intramolecular charge transfer state (TICT). The fluorescence quantum yield of the short wavelength emission is approximately 4 x 10(-4) at room temperature and increases by three orders of magnitude when the temperature is lowered to 80 K in accordance with the behavior of normal nucleic acid bases. In contrast, the long wavelength fluorescence quantum yield is almost temperature independent. The different photophysical processes for DMA are summarized into a kinetic scheme where the temperature quenching of the short wavelength fluorescence is exclusively through isomerization into the long wavelength emitting species. Direct internal conversion to the ground state, commonly believed to be the dominant process for nonradiative deactivation of the DNA bases, makes a negligible contribution for DMA.
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| 5. |
- Albinsson, Bo, 1963, et al.
(author)
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Matrix-isolation IR and UV spectra of Si3H8 and Si4H10: Isomers and conformers of oligosilanes
- 1996
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In: Journal of Physical Chemistry. - 0022-3654. ; 100:21, s. 8681-8691
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Journal article (peer-reviewed)abstract
- Matrix-isolation IR and UV spectra of Si3H8, i-Si4H10, and the two conformers of n-Si4H10 have been recorded. A quantitative separation of the IR spectrum of n-Si4H10 into contributions from the anti and gauche forms was accomplished by a combination of matrix annealing and selective monochromatic photodestruction experiments. A qualitative separation of their UV spectra was achieved as well. The IR spectra of Si3H8, i-Si4H10, and the two conformers of n-Si4H10 have been assigned by comparison with results of ab initio calculations, which reproduce the frequencies and even the relative intensities quite well. The calculations predict dihedral angles omega of 180 degrees and 57 degrees for the anti and the gauche conformer of n-Si4H10, respectively, and confirm earlier predictions of nearly equal stability for an isolated molecule. In the matrix, the anti conformer is more stable, The conformational effects on the UV spectrum of n-Si4H10 are not those anticipated from simple models of the Sandorfy or ladder C type, in that it is primarily not the energy but the intensity of the low-energy excited singlet states that depends strongly on the SiSiSiSi dihedral angle omega. This result is interpreted in terms of data from 6-in-8 CASSCF 6-31G* calculations, which predict an avoided crossing between a strongly allowed sigma sigma* B state and a very weakly allowed sigma pi* B state as omega changes, with the former lower in energy at 180 degrees and the latter lower at 0 degrees. Consequences for attempts to understand the effects of conformation on optical spectra of polysilanes are noted.
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| 6. |
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| 7. |
- Albinsson, Bo, 1963, et al.
(author)
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The origin of lignin fluorescence
- 1999
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In: Journal of Molecular Structure. - 0022-2860. ; 508:1-3, s. 19-27
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Journal article (peer-reviewed)abstract
- Spruce lignin exhibits fluorescence emission spectra that peaks at approximate to 360 nm on excitation at wavelengths ranging from 240 to 320 nm. This can be explained by non-radiative energy transfer from lignin chromophores, that are excited in the wavelength range 240-320 nm, to an acceptor that emits fluorescent Light at approximate to 360 nm. Examinations of lignin samples and model compounds suggest that small amounts of phenylcoumarone structures in the lignin is a conceivable acceptor. Such structures and stilbene structures are formed from structural elements in lignin of the phenylcoumaran type on various treatments. The photophysical properties of models for phenylcoumarone structures [2-(3,4-dimethoxyphenyl)-7-methoxy-3-methyo[b]-furan, 2-(3,4-dimethoxyphenyl)-3-hydroxymethyl-7-methoxybenzo[b]furan] and stilbene structures (the E and Z forms of 2-hydroxy-3,3',4'-trimethoxystilbene) have been examined and are discussed on the basis of crystal structure determinations. (C) 1999 Elsevier Science B.V. All rights reserved.
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| 8. |
- Andreasson, Joakim, 1973, et al.
(author)
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The photophysical properties of the adenine chromophore
- 1999
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In: Journal of Physical Chemistry B. ; 103:44, s. 9782-9789
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Journal article (peer-reviewed)abstract
- The efficient nonradiative deactivation process of the excited adenine chromophore is studied in this paper. By comparing the photophysical properties and temperature dependence of several alkylated adenine derivatives, a mechanism for the thermally activated internal conversion process is suggested, Several alkylamino derivatives of adenine show dual fluorescence, and the solvent dependence of the excited states is investigated. It is concluded that the long wavelength emission originates from a CT state involving the alkylamino group and purine chromophore as donor and acceptor, respectively. The experimental observations are supported by quantum mechanical calculations, and the results are summarized into a model for the photophysical properties of the adenine chromophore. In this model, the two excited states associated with the dual emission from the alkylamino derivatives are populated from a common Franck-Condon state followed by independent decay to the ground state.
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| 9. |
- Carlsson, C., et al.
(author)
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Experimental and simulated fluorescence depolarization due to energy transfer as tools to study DNA-dye interactions
- 1997
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In: Biopolymers. - 0006-3525 .- 1097-0282. ; 41:5, s. 481-494
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Journal article (peer-reviewed)abstract
- A method to study DNA-dye complexes by the combination of steady state fluorescence anisotropy measurements and computer simulations of the fluorescence depolarization due to resonance energy transfer is presented. The simulations are based on a Markov chain analysis, assuming random distribution of the dyes along the DNA chain and energy transfer that obeys Forster kinetics. Since the investigated intercalators (ethidium bromide, YO, PO) and groove binders [4'6-diamidino-2-phenylindole (DAPI)] were found to show different depolarization dependence on binding density, the method can be used to quite sensitively characterize the binding mode. Excellent agreement between the measured and simulated anisotropy is found for all investigated intercalators. The proposed method gives an estimation of the unwinding angle for intercalators and provides information about the binding site size, and the presence or absence of sequence specificity. For the groove binder DAPI interacting with mixed sequenced DNA, the measured and computed depolarization do not agree, and this can be rationalized in terms of the high sequence specificity of this dye. However, for DAPI bound to [poly(dA-dT)](2) the measured data agree well with computed data for a groove binder that is displaced a distance 7 Angstrom from the helix axis and has a binding site size of three bases. (C) 1997 John Wiley & Sons, Inc.
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| 10. |
- Holmén, Anders, 1967, et al.
(author)
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Assignment of electronic transition moment directions of adenine from linear dichroism measurements
- 1997
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 119:50, s. 12240-12250
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Journal article (peer-reviewed)abstract
- The electronic spectra of a series of adenine derivatives have been investigated with respect to the number of electronic transitions, their intensities, and transition moments. The experimental work includes linear dichroism (LD) measurements on samples partially oriented in stretched polymer poly(vinyl alcohol) films, fluorescence anisotropy (FA), and: magnetic circular dichroism (MCD). The UV spectra of both 7-methyladenine (7MA) and 9-methyladenine (9MA) are resolved into contributions from five pi --> pi* transitions (I-V). Their polarizations relative to the C-4-C-5 axis are for 7MA +45 degrees (I, 36 600 cm(-1)), -16 degrees (II, 39 500 cm(-1)), -28 degrees (III, 42 600 cm(-1)), +76 degrees (IV 45 800 cm(-1)) and similar to-29 degrees (V, similar to 47 700 cm(-1)); and for 9MA +66 degrees (I, 36 700 cm(-1)), +19 degrees (II, 38 820 cm(-1)), -15 degrees (III, 43 400 cm(-1)), -21 degrees (IV, 46 800 cm(-1)), and similar to-64 degrees (V, similar to 48 320 cm(-1)). The experimental results are correlated with results from semiempirical INDO/S and ab initio CIS/6-31G(d) and CASPT2 molecular orbital calculations. The transition moments are found to be conserved when the adenine amino group has been substituted with either one or two methyl groups. In addition, LD and MCD spectra for 6-(dimethylamino)-9-ethylpurine, which is soluble in nonpolar solvents, have been measured in stretched polyethylene film and cyclohexane, respectively. The results indicate that the electronic transition moments of the 9-substituted adenine chromophore are essentially the same in a polar and a nonpolar solvent. On the basis of the. results,for 7MA and 9MA, the reduced LD and absorption spectra of adenine are analyzed in terms of contributions from the 7-H and 9-H tautomers of adenine. By comparison with theoretical and experimental results for purine and 2-aminopurine regarding the position of the lowest n --> pi* transition, we are able to confidently position the lowest n --> pi* transition in 9MA very close to the lowest pi --> pi* transition. The proximity of the first (1)n pi* and (1) pi pi* states in adenine might be related to the efficient nonradiative deactivation of the lowest excited (1) pi pi* state.
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