The electronic spectrum of cytosine

Zaloudek, F.; Novros, Joel S.; Clark, Leigh B.

doi:10.1021/ja00311a022

Cited by 96 publications

(95 citation statements)

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“…Therefore, the emission yield of cytosine, rather than band position, is probably sensitive to a variety of external factors. On the blue side of the near-uv absorption domain, the "230-nm cytosine-type band"60 is predicted at 227-233 nm (in good agreement with all cytosine absorption spectra), followed by a very strong transition at 192-196 nm (in excellent agreement with band V of Zaloudek et al 55 and a moderately strong band at 181-185 nm ( a region apparently neglected by Zaloudek et al 55 as well as other authors). The 230-nm band appears to be a mixture of { a*,*} and { a*,n (0) } configurations, creating a narrowly split ( 100-250-cmp1) pair of transitions.…”

Section: Cytosinesupporting

confidence: 81%

Protein: Nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes

Ilich

Prendergast

1992

Biopolymers

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Low singlet transition energies and line strengths were calculated for the cytosine:indole:guanine complex by the INDO/1S-CI method. The chromophores were arranged in three sets of 270 intercalating geometries. Calculations were executed in the supermolecule model with single excited configurations. Errors due to basis set extension and incomplete configuration representation were assessed, for all chromophore pairs, by full BSSE correction calculations and inclusion of double-excited configurations. The intercalation-induced perturbations of the principal transitions are characterized by but not limited to (a) a decrease in strength of [pi*,pi] transitions, (b) increase in strength in [pi*,n] transitions, (c) splitting of [pi*,pi] transitions into components of unequal strength, and (d) energy and strength dependence in mixed transitions on rise and shift movements of the nucleic acid bases. These predictions are in accord with absorption, fluorescence emission, and scattering, and resonance Raman spectroscopic data on oligonucleotides and analogous aromatic complexes. The calculations suggest that major differences in intercalating coordinations are discernible in the near-uv spectroscopic domain of proteins and nucleic acids.

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Section: Cytosinesupporting

confidence: 81%

Protein: Nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes

Ilich

Prendergast

1992

Biopolymers

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“…Figure 2c is a schematic diagram indicating the orientations of the base transitions when the bases are linked to a simple backbone and the backbone is wrapped round the nanotube at an inclination angle of~458. The 230 nm region transitions of C [18] and A [24] are within 108 of the nanotube axis; this orientation would give a positive LD signal. The 244 and 200 nm transitions of G, [19] which will have some intensity at 230 nm, would also contribute a small positive signal, as oriented in Figure 2c.…”

Section: Resultsmentioning

confidence: 99%

The Binding of Single‐Stranded DNA and PNA to Single‐Walled Carbon Nanotubes Probed by Flow Linear Dichroism

Rajendra

Rodger

2005

Chemistry A European J

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The binding of single-stranded DNAs and a neutral DNA analogue (peptide nucleic acid, PNA) to single-walled carbon nanotubes in solution phase has been probed by absorbance spectroscopy and linear dichroism. The nanotubes are solubilised by aqueous sodium dodecyl sulfate, in which the nucleic acids also dissolve. The linear dichroism (LD) of the nanotubes, when subtracted from that due to the nanotubes/nucleic acid samples, gives the LD of the bound nucleic acid. The binding of the single-stranded DNA to the single-walled nanotubes is quite different from that previously observed for double-stranded DNA. It is likely that the nucleic acid bases lie flat on the nanotube surface with the backbone wrapping round the nanotube at an oblique angle in the region of 45 degrees . The net effect is like beads on a string. The base orientation with the single-stranded PNA is inverted with respect to that of the single-stranded DNA, as shown by their oppositely signed LD signals.

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“…In the present work, the MS(4)-CASPT2(12,9) excitation energy of the 1 ππ* state is calculated to be 4.48 eV, which agrees well with the experimental value of ~4.65 eV 53 in the gas phase as well as those in the other environments. [54][55][56] According to the oscillator strengths at the SA(4)-CASSCF(12,9) level, the 1 ππ* state is expected to be primarily populated by UV absorption. Our MS-CASPT2 calculations also exhibit that the two 1 nπ* states are characterized by modest mixing of the excitation from lone-pair orbitals centered on the O7 and N3 atoms, denoted as 1 n O π* and 1 n N π*, respectively.…”

Section: Vertical Excitation Energiesmentioning

confidence: 99%

Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

Nakayama

Harabuchi

Yamazaki

et al. 2013

Phys. Chem. Chem. Phys.

111

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A comprehensive picture of the ultrafast nonradiative decay mechanisms of three cytosine tautomers (amino-keto, imino-keto, and amino-enol forms) is revealed by high-level ab initio potential energy calculations using the multistate (MS) CASPT2 method and also by on-the-fly excited-state molecular dynamics simulations employing the CASSCF method. To obtain a reliable potential energy profile along the deactivation pathways, the MS-CASPT2 method is employed even for the optimization of minimum energy structures in the excited state and conical intersection (CI) structures between the ground and excited states. In the imino (imino-keto) form, we locate a new CI structure involving the twisting of the imino group, and the decay pathway leading to this CI is found to be barrierless, suggesting a remarkably efficient deactivation of imino cytosine. In the keto (amino-keto) form, the MS-CASPT2 calculations exhibit an efficient decay path to the ethylene-like CI involving the twisting of C-C double bond in the six-membered ring, with a barrier of ~0.08 eV from the minimum of the 1 ππ* state. In the enol (amino-enol) form, three types of CIs are identified for the first time. Among them, the ethylene-like CI with a similar molecular structure to the keto form provides the most preferred deactivation pathway of enol cytosine. This pathway exhibits a higher barrier of ~0.22 eV and a higher energy of CI than those of keto cytosine. Nonadiabatic molecular dynamics simulations provide a time-dependent picture of the deactivation processes, including the excited-state lifetime of each tautomer. In particular, the decay time of the imino tautomer is predicted to be only ~100 fs. Our computational results are in remarkably good agreement with the experimental findings in recent femtosecond pump-probe photoionization spectroscopy [J. Am. Chem. Soc. 131, 16939 (2009); J. Phys. Chem. A 115, 8406 (2011)], supporting the coexistence of more than one tautomer in the photophysics of isolated cytosine and that each tautomer exhibits a different excited-state lifetime.1

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The electronic spectrum of cytosine

Cited by 96 publications

References 0 publications

Protein: Nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes

Protein: Nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes

The Binding of Single‐Stranded DNA and PNA to Single‐Walled Carbon Nanotubes Probed by Flow Linear Dichroism

Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

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