Maciej J. Nowak

Matrix isolation studies of cytosine: The separation of the infrared spectra of cytosine tautomers

Abstract The i.r. spectral studies of cytosine and its d3-deuterated derivative isolated in Ar and Ne matrices are reported. The amino-hydroxy and the amino-oxo tautomeric forms dominate in matrices. Separation of the i.r. spectra of the two tautomers was based on observation of spectral changes following u.v. irradiation of the matrix. Detailed analysis and interpretation of the spectra was performed.

The infrared spectra of matrix isolated uracil and thymine : an assignment based on new theoretical calculations

Abstract The IR spectra of uracil and thymine predicted theoretically at the ab initio Hartree-Fock level with 6-31G basis set are reported and compared with Ar matrix experimental spectra. The IR spectra computed at the SCF/6-31G level reproduce the experimental spectra with an accuracy which allows a reliable vibrational assignment. A split valence basis set, augmented with polarization functions on all atoms, was found to be quite sufficient for a reliable prediction and assignment of the IR absorption bands in the spectra of medium-sized molecules.

Experimental matrix isolation and theoretical ab initio HF/6-31G(d, p) studies of infrared spectra of purine, adenine and 2-chloroadenine

Abstract The results of ab initio calculations at the Hartree—Fock level with the 6-31G( d , p ) basis set are reported for the harmonic vibrational infrared spectra of purine, adenine and 2-chloroadenine. These were compared with the experimental IR spectra of the compounds isolated in low-temperature matrices. The experimental spectra of 2-chloroadenine are reported for the first time. In the case of purine this comparison resulted in the complete assignment of the experimental IR spectrum. The proposed assignments of both the adenines studied are still incomplete.

A Computational Study on the Mechanism of Intramolecular Oxo−Hydroxy Phototautomerism Driven by Repulsive πσ* State

Potential energy (PE) surfaces of the lowest excited states of the 4(3H)-pyrimidinone/4-hydroxypyrimidine system were investigated with the aid of the CC2 and CASSCF methods of the electronic structure theory. These studies resulted in identification of a low-lying pi sigma* state, which is dissociative with respect to the stretching of the N-H or O-H bonds in the oxo and hydroxy structures of the compound, respectively. After initial excitation to the lowest local n pi* and/or pi pi* singlet states, the system can access the PE surface of the pi sigma* state by crossing a low barrier. It was computationally demonstrated that the system should evolve on the PE surface of the repulsive pi sigma* state toward a broad seam of intersection with the PE surface of the ground state. At the intersection, the nonadiabatic transition to the ground electronic state takes place and the system can either evolve to a minimum of the initially excited tautomer or to the ground-state minimum of the other tautomer. The steps listed above provide a mechanism of photoinduced dissociation-association (PIDA) phototautomerism, experimentally observed for a number of monomeric molecules, structurally similar to 4(3H)-pyrimidinone/4-hydroxypyrimidine. This mechanism describes a new class of intramolecular phototautomeric reactions driven by a repulsive pi sigma* state.

INFRARED MATRIX ISOLATION SPECTRA OF 1-METHYLURACIL. REVISED ASSIGNMENT BASED ON THE HARTREE-FOCK AND POST-HARTREE-FOCK STUDIES

Abstract Ab initio calculations of the infrared spectra of 1-methyluracil have been carried out with the Hartree–Fock and the second order Moller–Plesset perturbation (MP2) methods using the D95V** basis set. Theoretical harmonic frequencies and absolute infrared intensities reproduce well the experimental infrared spectra of the Ar matrix isolated species. The revised assignment of the infrared spectra of monomeric 1-methyluracil isolated in Ar and N2 matrices is presented.

Tautomeric equilibria of 2(4)-monooxopyrimidines in the gas phase, in low-temperature matrices and in solution

Abstract IR absorption spectra, including the NH, OH and CO stretching regions, have been recorded for 4-oxo-6-methyl- and 2-oxo-4,6-dimethyl pyrimidines and several related derivatives, in the gas phase, in low-temperature inert matrices, and in several liquid solvents. All the 4-oxopyrimidines in the gas phase, and 4-oxo-6-methylpyrimidine in low-temperature matrices, exhibit comparable populations of the keto and enol forms. By contrast the 2-oxopyrimidines are predominantly in the enol forms. Both classes of com pounds are predominantly in the keto form in liquid solvent systems. The tautomeric equilibrium constant ( K T ) in the vapour phase for 4-oxo-2,6-dimethylpyrimidine is about 2, and for the other 4-oxopyrimidines is about 1. For 4-oxo-6-methylpyrimidine, the equilibrium constant in inert matrices varies slightly with the activity of the matrix gas, with the keto tautomer favoured in the more active matrix. From the temperature-dependence of K T the free energy difference between the two tautomeric forms of 4-oxo-6-methylpyrimidine in the vapour phase has been calculated. Heats of vaporization have also been calculated for the various compounds and related to their abilities to associate by hydrogen bonding in the condensed phase. The UV absorption spectra of some of the foregoing have also been recorded in the gas phase, but these were of only limited value in studies of tautomeric equilibria, as connpared to the IR spectra.

IR matrix isolation studies of nucleic acid constituents: the spectrum of monomeric thymine

Abstract The IR matrix isolation spectra of thymine and N 1 , N 3 -dideuterated thymine in argon and nitrogen matrices are reported. The spectra are interpreted by comparison with the previously assigned spectra of uracil. The frequencies of the NH stretching and bending modes are not much changed on methyl substitution in the 5-position of the uracil ring. The most pronounced differences are observed in the frequency region of the ring vibrations.

An infrared matrix isolation study of tautomerism in purine and adenine

Abstract Contrary to previous interpretations of the infrared spectra of purine and adenine isolated in low-temperature argon matrices suggesting that the molecules exist as a mixture of two tautomeric forms N(9)H and N(7)H of comparable weights, reinvestigation of the vibrational spectra in inert matrices (neon, argon, nitrogen) suggests that the observed IR absorption is due to one tautomeric form of either purine or adenine. This is in agreement with ab initio quantum-mechanical calculations of the relative internal energies of purine and adenine tautomers which predict the N(9)H tautomer to be the most stable form in both cases.

Infrared matrix isolation and ab initio quantum mechanical studies of purine and adenine

Abstract Results are presented from ab initio SCF (3-21G) calculations for the geometries of the N(9)H and N(7)H tautomers of purine and adenine and vibrational spectra (wavenumbers and intensities) of the N(9)H forms. All these results are compared with available geometries from crystallographic studies and with reported infrared spectra of the molecules isolated in inert gas low-temperature matrices. The N(9)⇌N(7)H tautomerism of the molecules in question is also briefly discussed.

Matrix isolation studies of nucleic acid constituents—III. 1-Methyluracil, 3-methyluracil and 1,3-dimethyluracil monomers

Abstract Infrared spectral studies are reported for 1-methyluracil and its N 3 -deuterated homologue and also for 3-methyl- and 1,3-dimethyluracil, all isolated in argon matrices. The effects of N 3 -deuteration, and of methylation at N 1 and N 3 , on the spectrum of the parent uracil molecule are profound and have been investigated in detail. It is shown that the frequencies and relative intensities of the vibrational bands in the spectrum of the monomeric molecules exhibit a complicated dependence on N -deuteration or N -methylation. The spectra are interpreted by comparison with the predicted spectra using force constants and intensity parameters (APTs) from quantum mechanical ab initio calculations with STO-3G (force constants) and 4–31G (intensities) basis sets of the i.r. spectrum for the in-plane modes of uracil. Appropriate corrections were taken into account so that these predictions apply to the deuterated and methylated uracils.