1. |
- Holmén, Anders, 1967, et al.
(författare)
-
Assignment of electronic transition moment directions of adenine from linear dichroism measurements
- 1997
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 119:50, s. 12240-12250
-
Tidskriftsartikel (refereegranskat)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.
|
|
2. |
- Holmén, Anders, 1967, et al.
(författare)
-
Ir Transition Moments of 1,3-Dimethyluracil - Linear Dichroism Measurements and Ab-Initio Calculations
- 1994
-
Ingår i: Journal of Physical Chemistry. - 0022-3654. ; 98:19, s. 4998-5009
-
Tidskriftsartikel (refereegranskat)abstract
- The vibrational transition moment directions of 1,3-dimethyluracil (DMU), 1,3-dimethyluracil-5-d (DMU-5-d), and 1,3-dimethyluracil-6-d (DMU-6-d) have been determined from measurements of polarized IR spectra on samples partially aligned in stretched poly(vinyl alcohol) and by ab initio calculations at the HF/6-31G* level of approximation. The agreement between experiments and theory is good. IR spectra of DMU, DMU-5-d, and DMU-6-d in KBr and in D2O form, together with the calculated spectra and the IR polarizations, the basis for some reassignments. Special attention is paid to the double-bond region, where the high-frequency carbonyl stretching mode is assigned to an in-phase vibration of the C4O and the C2O. This vibration is polarized in a direction almost bisecting the angle between the two carbonyl bonds, in agreement with an in-phase assignment. The low-frequency mode is the out-of-phase vibration of the two carbonyl groups, and it is consequently polarized perpendicular to the high-frequency mode. In order to determine the orientation axis of DMU in the polymer matrix, the UV linear dichroism (LD) spectrum was measured and the polarizations of the electronic transitions were estimated from a semiempirical self-consistent reaction field (SCRF) calculation including solvent effects. The combined information from IR LD and UV LD shows that the molecular orientation axis in the stretched film experiment is parallel to the first pi --> pi* transition in DMU.
|
|
3. |
- Colmenarejo, G., et al.
(författare)
-
Electronic Spectra and Transition Moments of 6-(2’-Pyridiniumyl)phenanthridinium Photoactive DNA Intercalators
- 1997
-
Ingår i: Journal of Physical Chemistry B Materials. - : American Chemical Society (ACS). - 1089-5647 .- 1520-6106 .- 1520-5207. ; 101:26, s. 5196-5204
-
Tidskriftsartikel (refereegranskat)abstract
- The electronic transitions giving rise to the UV-visible absorption spectra of two pyridinium-phenanthridinium viologens, 6,7-dihydropyridol[2',1':3,4]pyrazinol[1,2-f]phenanthridinediium dication (1) and 7,8-dihydro-6H-pyrido[2',1':3,4]diazepino[1,2-f]phenanthridinediium dication (2), have been investigated with respect to energies, intensities, and transition moment directions. A combination of methods has been applied: UV-visible absorption, circular dichroism, magnetic circular dichroism, fluorescence anisotropy, Linear dichroism In stretched poly(vinyl alcohol) films, and semiempirical molecular orbital calculations. For both drugs, the lowest energy absorption band, occurring around 400 nm, results from two separate transitions. The corresponding electric transition dipole moments lie in the phenanthridine plane and are polarized, respectively, in the direction of the pyridine moiety (the lower energy transition) and parallel to the phenanthridine long axis (the higher energy transition). Up to four additional different pi --> pi* transitions account for a second band that peaks at 250 nm; they show different polarizations within the phenanthridine plane. The lowest energy transition of the whole spectrum of both drugs corresponds to the promotion of an electron from the HOMO to the LUMO, which are molecular orbitals mainly localized in the phenanthridine and pyridine rings, respectively, thereby implying a charge transfer, upon excitation, from the phenanthridine toward the pyridine ring. The experimental and theoretical results are discussed in relation to the spectroscopic, redox, and photochemical properties of these drugs.
|
|
4. |
- Gawronski, J., et al.
(författare)
-
Excited States of the Phthalimide Chromophore and Their Exciton Couplings: A Tool for Stereochemical Assignments
- 1998
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 120:46, s. 12083-12091
-
Tidskriftsartikel (refereegranskat)abstract
- The electronically excited states of the phthalimide chromophore have been studied by means of linear dichroism (LD) of samples partially oriented in poly(vinyl alcohol) films, magnetic circular dichroism (MCD), and circular dichroism (CD) spectroscopy. On the basis of the LD measurements, the low-energy tail (340-320 nm) of the first absorption band is assigned to an out-of-plane polarized pi-->pi* transition (I). At higher energy, the electronic spectrum is resolved into contributions from five pi-->pi* transitions: II(300 nm, long-axis polarized), III (275 nm, short-axis polarized), IV (235 nm, short-axis polarized), V (220 nm, long-axis polarized), and VI (similar to 210 nm, short-axis polarized). The results from semiempirical (INDO/S-CI) and ab initio (CIS/6-31+G(d)) MO calculations compare well with the proposed assignments of the excited states. Degenerate exciton interaction between electric-dipole-allowed transitions of two phthalimide chromophores is observed in the electronic absorption spectra of the achiral bis-phthalimides 2a-c and in the CD spectrum of the chiral bis-phthalimide 3a. For the latter compound, the solid-state geometry has been determined by X-ray diffraction analysis. Good agreement between experimental and computed CD spectra confirms that the coupled-oscillator exciton model provides the basis for a reliable nonempirical method for the assignment of absolute configuration for this class of compounds. Nondegenerate exciton coupling between phthalimide and benzoate or phenyl chromophores is born out in the CD spectra of homochiral molecules 3c and 3d with the rigid cyclohexane skeleton. Finally, the exciton coupling method is used to make stereochemical assignments for the acyclic, conformationally flexible derivatives 4a-c and 5b.
|
|
5. |
- Holmén, Anders, 1967, et al.
(författare)
-
ELECTRONIC-TRANSITION DIPOLE-MOMENTS OF THE 1,N-6-ETHENOADENINE CHROMOPHORE
- 1994
-
Ingår i: Journal of Physical Chemistry. - : American Chemical Society (ACS). - 0022-3654 .- 1541-5740. ; 98:51, s. 13460-13469
-
Tidskriftsartikel (refereegranskat)abstract
- The electronic spectra of 1,N-6-ethenoadenine (epsilon-adenine, epsilon-A), 3-methyl-epsilon-adenine (3-me-epsilon-A), and epsilon-adenosine (epsilon-Ado) have been examined with respect to the number of electronic transitions, their intensities, and their transition moments, on the basis of measurements of UV and IR linear dichroism (LD) on samples partially oriented in stretched poly(vinyl alcohol) films, fluorescence anisotropy (FA), and magnetic circular dichroism (MCD). The experimental results are compared with semiempirical molecular orbitaI calculations. Four pi-->pi(*) transitions were found to contribute to the UV spectrum of the epsilon-adenine chromophore with the following transition moment directions (relative to the ''adenine'' pseudosymmetry long axis, counted toward N-1): +27 degrees +/- 10 degrees (I at 32 500 cm(-1)), -47 degrees +/- 5 degrees (II at 37 000 cm(-1)), -30 degrees +/- 10 degrees (III at 32 000 cm(-1)), and -11 degrees +/- 10 degrees or -49 degrees +/- 10 degrees (IV at approximate to 46 000 cm(-1)). The orientation parameters in the stretched film experiments were determined from polarized IR measurements combined with UV LD and FA data. In addition, fluorescence emission and excitation spectra and fluorescence lifetimes of E-A in aqueous solutions indicate that epsilon-A does not behave as a single spectroscopic species. In contrast to 3-me-epsilon-A and epsilon-Ado, epsilon-A displays an emission wavelength dependent excitation spectrum and a biexponential fluorescence decay. This observation is attributed to a prototropic tautomeric equilibrium between the 1-H and 3-H forms of epsilon-A.
|
|
6. |
- Holmén, Anders, 1967, et al.
(författare)
-
Electronic transition moments of 2-aminopurine
- 1997
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 119:13, s. 3114-3121
-
Tidskriftsartikel (refereegranskat)abstract
- The electronic spectrum of the unnatural nucleic acid base 2-aminopurine is important in order to understand the spectroscopy and photophysics of the normal DNA bases. Knowledge of transition moment directions and effective absorption components is also a prerequisite for the interpretation of emission spectra of 2-aminopurine incorporated into DNA as a probe of nucleic acid base motion or excitation energy transfer processes. Using linear dichroism, fluorescence anisotropy, and ordinary and magnetic circular dichroism techniques, the near-UV spectrum of 2-aminopurine is resolved into contributions from five electronic transitions. Four moderately strong pi-->pi* transitions (I, III, IV, and V) are observed, polarized at +53 degrees (I), -72 degrees (III), -77 degrees (IV), and +57 degrees or -67 degrees (V) relative to the short molecular axis. In addition, one weak n --> pi* transition (II) polarized perpendicular to the molecular plane has been identified. Semiempirical INDO/S calculations support these assignments.
|
|
7. |
- Holmén, Anders, 1967
(författare)
-
Excitation and Ground-State Properties of Natural and Modified Nucleic Acid Bases
- 1997
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The nucleic acid bases are the carriers of genetic information in DNA and RNA. They are also the main chromophores of nucleic acids and determine their optical properties and sensitivity to UV radiation. In order to understand and interpret the optical spectra and photophysical behavior of nucleic acid bases, this thesis focuses on the electronic and vibrational transition moments of the naturally occurring nucleic acid bases uracil and adenine, and two synthetic, fluorescent bases: 1,N6-ethenoadenine and 2-aminopurine. The tools have been linear dichroism, fluorescence anisotropy and magnetic circular dichroism techniques in combination with semi-empirical molecular orbital calculations of electronic spectra, and ab initio and density functional theory (DFT) calculations of vibrational spectra. The UV spectrum of adenine is concluded to derive from five .pi. - .pi.* transitions whose transition moment directions and band shapes are characterized. The presence of an .pi. - .pi.* transition occurring close to the lowest .pi. - .pi.* transition is inferred from comparisons with other purines and from quantum-chemical calculations. Such an .pi. - .pi.* transition could explain the low fluorescence quantum yield and also the relatively low photochemical reactivity of adenines. For 1,N6-ethenoadenine and 2-aminopurine, the UV spectra are resolved into contributions from four .pi. - .pi.* transitions. A most remarkable finding in 2-aminopurine is the identification of a low-lying .pi. - .pi.* transition. The determined transition moments should be useful for studies of structure and dynamics of nucleic acids based on absorption and emission anisotropy. The carbonyl stretching vibrations of 1,3-dimethyluracil are assigned to the in-phase and out-of-phase components of the carbonyl stretching motions. The transition moment directions of the strong amino-group-scissoring and ring-stretching vibrations in adenine and 2-aminopurine are expected to be useful for structural studies of nucleic acids containing adenine or 2-aminopurine bases using IR spectroscopy. Some of the purines are investigated with respect to their structures and tautomerism in solution using ab initio and DFT calculations. The results allow us to predict relative concentrations of various tautomers, and to identify possible differences between solution and gas-phase structures and those determined by crystallographic methods.
|
|
8. |
- Holmén, Anders, 1967, et al.
(författare)
-
Thermodynamics of PNA-Nucleic Acid Interactions
- 1999
-
Ingår i: Peptide Nucleic Acids: Protocolls and Applications (eds. Peter E. Nielsen, Michael Egholm). - 1898486166 ; , s. 87-97
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
9. |
- Ratilainen, Tommi, 1970, et al.
(författare)
-
Hybridization of peptide nucleic acid
- 1998
-
Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 37:35, s. 12331-12342
-
Tidskriftsartikel (refereegranskat)abstract
- The thermodynamics of hybridization and the conformations of decameric mixed purine-pyrimidine sequence PNA/PNA, PNA/DNA, and DNA/DNA duplexes have been studied using fluorescence energy transfer (FET), absorption hypochromicity (ABS), isothermal titration calorimetry (ITC), and circular dichroism (CD) techniques. The interchromophoric distances determined in the FET experiments on fluorescein- and rhodamine-labeled duplexes indicate that the solution structures of the duplexes are extended helices in agreement with available NMR (PNA/DNA) and crystal X-ray data (PNA/PNA). The melting thermodynamics of the duplexes was studied with both FET and ABS. The thermodynamic parameters obtained with ABS are in good agreement with the parameters from calorimetric measurements while FET detection of duplex melting gives in most cases more favorable free energies of hybridization. This discrepancy between FET and ABS detection is ascribed to the conjugated dyes which affect the stability of the duplexes substantially. Especially, the dianionic fluorescein attached via a flexible linker either to PNA or to DNA seems to be involved in an attractive interaction with the opposite dicationic lysine when hybridized to a PNA strand. This interaction leads to an increased thermal stability as manifested as a 3-4 degrees C increase of the melting temperature. For the PNA/DNA duplex where fluorescein is attached to the PNA strand, a large destabilization (Delta T-m = -12 degrees C) occurs relative to the unlabeled duplex, probably originating from electrostatic repulsion between the fluorescein and the negatively charged DNA backbone. In the case of the PNA/PNA duplex, the sense of helicity of the duplex is reversed upon conjugation of fluorescein via a flexible linker arm, but not when the fluorescein is attached without a linker to the PNA.
|
|
10. |
- Son, G.S., et al.
(författare)
-
Binding Mode of Norfloxacin to Calf Thymus DNA
- 1998
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 120:26, s. 6451-6457
-
Tidskriftsartikel (refereegranskat)abstract
- Norfloxacin, a quinolone antibacterial reagent, has been studied with respect to its binding to calf thymus DNA using fluorescence and linear dichroism techniques and unwinding of supercoiled DNA. The fluorescence of norfloxacin is strongly quenched in the presence of DNA and using this decrease in a fluorescence titration the equilibrium constant of the complex formation was established to be 2.8 x 10(3) M-1. The electric transition moments of the norfloxacin chromophore have been analyzed using fluorescence anisotropy, magnetic circular dichroism, and linear dichroism in stretched poly(vinyl alcohol) film and INDO/S calculations. These data are then used to interpret flow linear dichroism results for the norfloxacin-DNA complex. The transition moments for the long-wavelength transitions are found to be oriented at about 65.0-85.0 degrees with respect to the DNA helix axis. A near perpendicular orientation of the norfloxacin chromophore plane makes it possible to exclude classical groove or surface binding modes. The possibility of a classical intercalation binding mode also can be ruled out from unwinding experiments. However, it is shown that the molecular plane of norfloxacin is near perpendicular relative to the DNA helix axis with a possibility of a bending of the DNA helix at the binding site.
|
|