Theoretical study of electronic spectra and photophysics of uracil derivatives

The changes that the UV absorption spectrum and the photophysics of uracil undergo under hydrogen substitution or deprotonation, were studied theoretically within the CS-INDO/CI scheme. First of all this method was tested on uracil. It was then used for the calculation of the electronic structure of excited states (Sn, Tn) of a large number of uracil derivatives (1-, 3- and 5-methyluracil; 1,3-, 1,5- and 3,5-dimethyluracil; 5-fluoro- and 5-chlorouracil), including some anions (1- and 3-methyluracil anion). The excited states were obtained in the singly-excited configuration interaction approximation (S-CI) and the correlation effects on (pi pi*) states were studied by including the most important doubly- and triply-excited configurations in the CI. The S-CI wavefunctions were used for the calculation of the most important electronic matrix elements for spin-orbit coupling. The photophysics of these compounds is discussed using Jablonski diagrams.     

Theoretical study of the shifts of electronic spectra from solute-solvent interaction

Previous theories of spectral solvent shifts are briefly discussed. The basic dipole approximation is analyzed both theoretically and in relation to experimental information. On account of the restricted validity of this approximation — especially for molecules consisting of several polar groups — another, electrostatic model, originating from the Born charging, is investigated. This model is applied to semi-empirical PPP-calculations of spectral solvent shifts of some quinones. Among other things, this model predicts that not only n → π⁸ transitions may be blue shifted but also certain π → π* transitions. When the electrostatic effect is small, other terms may be responsible for the solvent shift, e.g. polarizability. The cavity effect is not expected to be important in the present context.     

Microscopic solvent shifts in the electronic spectra of large van der waals molecules

The experimental red-shifts of the electronic origins of a number of large non-polar van der Waals molecules are reported. A comparison with the theoretical red-shifts calculated by a formalism given by Longuet-Higgins and Pople yields a good correlation, reflecting the dominant role of dispersion interactions in these complexes.     

Electronic spectra of uracil in a supersonic jet

The fluorescence excitation and dispersed fluorescence spectra of uracil in a supersonic jet have been observed. The n,π¹ states of 2,4-diketo tautomer and enol-keto tautomer are found. The spectral analyses show an out-of-plane deformation of the molecules in the n,π¹ state. The coexistence of diketo and enol-keto tautomer in the vapor is discussed.     

Mass spectra of bromohydrins of uracil derivatives

The mass fragmentation of bromohydrins of uracil derivatives is discussed. Fragmentation pathways have been proposed on the basis of high-resolution data and metastable transitions. The distinct influence of substituents in position 5 of uracil on the fragmentation pathway has been observed.     

Lanthanide-induced shifts in proton NMR spectra of cyclohexanones

The lanthanide-induced shifts (LIS) of the lanthanide shift reagent (LSR) Eu(FOD)₃ are reported for a large number of cyclohexanones, especially those which are highly substituted. The following compounds were synthesized and characterized: 3-(aryl)-3,5,5-trimethylcyclohexanones, in which aryl = 1-naphthyl, phenyl, o-anisyl, m-anisyl, p-anisyl and p-chlorophenyl. Some analogous compounds were also studied: 3,5,5-trimethylcyclohexanone, 4-tert-butyl-cyclohexanone, 3,3,5,5-tetramethylcyclohexanone 3-(1-naphthyl)5,5-dimethylcyclohexanone and para-tert-butyl-anisole. A method for the regression analysis of the concentration dependence of the LIS of these substrates is developed and reported, and used to derive the limiting incremental LIS (Δ₂) for the LS₂ complex and to evaluate the proton chemical shifts (δ₀) in the absence of LSR. An ‘incremental dilution’ technique was found to be most appropriate to insure constant substrate concentrations, needed to extract both Δ₂ and δ₀. The conformations of the 3-(aryl)-type systems and analogous compounds were studied via LIS and found to conform to:—(i) an axially disposed aryl substituent in the 3,3,5,5-tetra-substituted cyclohexanones and (ii) a flattened chair form of the cyclohexanone ring with distortions in this chair form being an increase in the syn-diaxial (C-3, C-5) substituent distance (C-3 and C-5 substituents still eclipsed). The LIS were fully compatible with these structural assumptions.     

Connection between the electronic structure of tin in its compounds and the isomer shifts in the Mössbauer spectra

A formula is obtained which relates the isomer shifts in the Mössbauer spectra to the electronic structure of tin in its compounds. It is shown that these formulas describe the isomer shifts of various kinds of chemical compounds: tetravalent tin with -bonding (tin tetrahalides), tetravalent tin with no -bonding (compounds in which the tin is bound to alkyl, aryl, or metal carbonyl radicals), divalent tin, etc. The formulas are used to analyze the electronic structures of tin in compounds of these classes. It is shown that in tetravalent tin compounds with -bonding the isomer shift in the negative direction (with respect to -Sn) is due to the decreased number of 5s-valence electrons, and in the absence of -bonding, by an increase in the number of 5s-valence electrons.     

Infrared spectra of protonated uracil, thymine and cytosine.

The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.     

Lanthanide-ion-induced paramagnetic shifts in NMR spectra in aqueous solutions

Theoretical and Experimental Chemistry -     

Ab initio calculations of the ultraviolet resonance Raman spectra of uracil

An equation been derived to calculate, ab initio, the frequencies and intensities of a resonant Raman spectrum from the transform theory of resonance Raman scattering. This equation has been used to calculate the intensities of the ultraviolet resonance Raman spectra from the first π-π* excited state of uracil and 1,3-dideuterouracil. The protocol for this calculation is as follows: (1) The force constant matrix elements in Cartesian coordinate space, the vibrational frequencies, and the minimum energy ground and excited state geometries of the molecule are calculated ab initio using the molecular orbital program Gaussian 92, (2) the force constants in Cartesian coordinates are transformed into force constants in the space of a set of 3N – 6 nonredundant symmetrized internal coordinates, (3) the G matrix is constructed from the energy minimized ground state Cartesian coordinates and the GFL = LΛ eigenvalue equation is solved in internal coordinate space, (4) the elements of the L and L^?1 matrices are calculated, (5) the changes in all of the internal coordinates in going from the ground to the excited state are calculated, and (6) these results are used in combination with the transform theory of resonance Raman scattering to calculate the relative intensities of each of the 3N – 6 vibrations as a function of the exciting laser frequency. There are no adjustable parameters in this calculation, which reproduces the experimental frequencies and intensities with remarkable fidelity. This indicates that the Dushinsky rotation of the modes in the excited state of these molecules is not important and that the simplest form of the transform theory is adequate. © 1995 John Wiley & Sons, Inc.     

Isotropic chemical shifts in magic-angle spinning NMR spectra of proteins

Here we examine the effect of magic-angle spinning (MAS) rate upon lineshape and observed peak position for backbone carbonyl (C') peaks in NMR spectra of uniformly-(13)C,15N-labeled (U-(13)C,15N) solid proteins. 2D N-C' spectra of U-(13)C,15N microcrystalline protein GB1 were acquired at six MAS rates, and the site-resolved C' lineshapes were analyzed by numerical simulations and comparison to spectra from a sparsely labeled sample (derived from 1,3-(13)C-glycerol). Spectra of the U-(13)C,15N sample demonstrate large variations in the signal-to-noise ratio and peak positions, which are absent in spectra of the sparsely labeled sample, in which most 13C' sites do not possess a directly bonded 13CA. These effects therefore are a consequence of rotational resonance, which is a well-known phenomenon. Yet the magnitude of this effect pertaining to chemical shift assignment has not previously been examined. To quantify these effects in high-resolution protein spectra, we performed exact numerical two- and four-spin simulations of the C' lineshapes, which reproduced the experimentally observed features. Observed peak positions differ from the isotropic shift by up to 1.0 ppm, even for MAS rates relatively far (a few ppm) from rotational resonance. Although under these circumstances the correct isotropic chemical shift values may be determined through simulation, systematic errors are minimized when the MAS rate is equivalent to approximately 85 ppm for 13C. This moderate MAS condition simplifies spectral assignment and enables data sets from different labeling patterns and spinning rates to be used most efficiently for structure determination.     

High-resolution electronic spectra of ethylenedioxythiophene oligomers

The photophysical properties of a series of 3,4-ethylenedioxythiophene oligomers (OEDOT) with up to five repeat units are studied as function of conjugation length using absorption, fluorescence, phosphorescence, and triplet-triplet absorption spectroscopy at low temperature in a rigid matrix. At 80 K, a remarkably highly resolved vibrational fine structure can be observed in the all electronic spectra which reveals that the electronic structure of the oligomers strongly couples to two different vibrational modes (approximately 180 and approximately 50 meV). The energies of the 0-0 transitions in absorption, and fluorescence, phosphorescence, and triplet-triplet absorption all show a reciprocal dependence on the inverse number of repeat units. The triplet energies inferred from the phosphorescence spectra are accurately reproduced by quantum chemical DFT calculations using optimized geometries for the singlet ground state (S0) and first excited triplet state (T1). Using vibrational IR and Raman spectroscopy and quantum chemical DFT calculations for the normal modes in the ground state, we have been able to assign the vibrations that couple to the electronic structure to fully symmetric normal modes. The high-energy mode is associated with the well-known carbon-carbon bond stretch vibration, and the low-energy mode involves a deformation of the bond angles within the thiophene rings and a change of C-S bond lengths. Experimentally obtained Huang-Rhys parameters and theoretical normal mode deformations are used to analyze the geometry changes between T1 and S0 and to semiexperimentally predict the geometry in the S1 state for 2EDOT.     

Vibrational spectra and structure of 5,6-diamino uracil and 5,6-dihydro-5-methyl uracil by density functional theory calculations

The molecular vibrations of 5,6-diamino uracil and 5,6-dihydro-5-methyl uracil were investigated in polycrystalline sample, at room temperature, by FT-IR and FT-Raman spectroscopies. The spectra were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculations based on the density functional theory (DFT) using standard B3LYP/6-31G* and B3LYP/6-311+G** methods and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compounds. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.