Near-IR-Induced, UV-Induced, and Spontaneous Isomerizations in 5-Methylcytosine and 5-Fluorocytosine

Abstract

Monomeric 5-methylcytosine (5mCyt) and 5-fluorocytosine (5FCyt) were studied using the matrix-isolation method. In 5mCyt and 5FCyt, the most stable form, dominating in low-temperature matrixes, is the amino-hydroxy (AH) tautomer. For both compounds, irradiation of the matrixes with near-IR laser light or with broadband near-IR or mid-IR light induces interconversions between the two rotamers of tautomer AH. In addition, for matrixes kept in darkness, a spontaneous tunneling conversion of the higher-energy hydroxy conformer (with the OH group directed toward the N3 atom) into the lower-energy form (OH directed toward N1) was occurring, with half-life time of 70 min for 5mCyt and 127 min for 5FCyt. These tunneling processes are much faster than that found for unsubstituted cytosine, where the half-life time is more than 30 h. UV irradiation of 5mCyt (at 316 nm) led to phototautomeric conversion of the amino-oxo form into the amino-hydroxy tautomer. Another phototransformation induced by irradiation of 5mCyt at 316 nm was the cleavage of the C-N bond in the amino-oxo form, resulting in generation of the open-ring conjugated isocyanate product. Irradiation of 5mCyt at shorter waves (λ ≤ 310 nm) induced the syn-anti photoisomerization within the imino-oxo forms of the compound. For matrix-isolated 5FCyt, the amount of the amino-oxo form was very small (with respect to the amino-hydroxy tautomer), while the imino-oxo isomers were not detected at all.

Narrowband NIR-Induced In Situ Generation of the High-Energy Trans Conformer of Trichloroacetic Acid Isolated in Solid Nitrogen and its Spontaneous Decay by Tunneling to the Low-Energy Cis Conformer

“…As found for other carboxylic acids [2,3,[7][8][9][10][13][14][15] (and also other molecules bearing the OH fragment) [5,6,11,12] spontaneous conversion of trans-TCA into cis-TCA, by tunneling, was observed, as noticed by the decrease of intensity of the bands ascribed to trans-TCA and simultaneous recover of bands due to the cis form. Figure 5 shows the evolution with time of the intensity of the νC=O stretching band of trans-TCA (1818-1812 cm -1 range), where the intensity of the band in the last spectrum resulting from near-IR irradiation at 6898.5 cm -1 was normalized to unity.…”

“…[2][3][4] It is now possible to choose the vibrational mode used to excite the targeted precursor conformer in a very selective way, [2][3][4][5][6][7][8] and since then many successful examples of application of the technique have been reported. [2][3][4][5][6][7][8][9][10][11][12] In several cases, the application of the method aims to generate high-energy rare conformers otherwise inaccessible to experiment. [2][3][4][5][6][8][9][10][11][12] A conformational isomerisation occurs when enough energy is deposited into the reaction coordinate, so that the system can overcome the energy barrier and pass into the products valley.…”

“…[2][3][4][5][6][7][8][9][10][11][12] In several cases, the application of the method aims to generate high-energy rare conformers otherwise inaccessible to experiment. [2][3][4][5][6][8][9][10][11][12] A conformational isomerisation occurs when enough energy is deposited into the reaction coordinate, so that the system can overcome the energy barrier and pass into the products valley. The reaction coordinate for internal rotation around a single bond connecting two conformers is essentially described by the torsion about that bond.…”

“…Alternatively, energy is introduced in the molecule by excitation of a different higher-energy vibration with appreciable absorption cross section. [2][3][4][5][6][7][8][9][10][11][12] This energy is then partially transferred to the reaction coordinate through a cascade relaxation mechanism involving participation of matrix phonons.…”

“…[2][3][4]7,9,[13][14][15][16] Together with additional studies on other molecules, these investigations allowed to reach some general conclusions: i) in general, once formed, the highenergy conformer of the carboxylic acids convert back spontaneously to the more stable form by tunnelling, even at cryogenic temperatures, in time scales that vary from a few seconds to several hours; [7,8,[13][14][15][16] ii) the stability of the higher-energy forms depends upon several factors, the dominant one appearing to be the height/wideness of the energy barrier separating the higher energy form from the lower energy one; [3,7,14] iii) specific interactions with the matrix material affect also the stability of the higher-energy form, which has been found to be greater in solid N2 and CO2 than in rare gases; [7,8,14,15] iv) differences in the matrix microenvironments also influence the life-time of the higher-energy conformer, even if they appear spectroscopically indistinguishable, leading to decay rates that very often obey to a dispersive-type kinetics instead of following a single exponential behaviour. [5][6][7][8][9][10][11][12] The present study focuses on trichoroacetic acid (Cl3CCOOH; TCA), which differs from acetic acid by replacement of the methyl group by the strongly electron-attractor trichloromethyl moiety. Such structural modification can be expected to lead to a reduction of the double bond character of the carboxylic C-O bond, implying a lower energy barrier for the trans → cis conformational isomerization in TCA, and reducing the stability of the higher-energy trans conformer (O=C-O-H dihedral angle: 180°; see Figure 1) once it is generated in a suitable matrix media using the strategy presented above.…”