Molecular orbital theory of the hydrogen bond. 24. Ground-state water–uracil complexes

Ab initio SCF calculations with the STO -3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water–uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N₁? H and O₂, N₃? H and O₂, and N₃? H and O₄. Open structures form at O₄, N₁? H, and N₃? H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N₁? H and the cyclic one at N₁? H and O₂. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N₃? H and a cyclic structure at N₃? H and O₄. The third cyclic structure at N₃? H and O₂ collapses to the “wobble” dimer at N₃? H and O₄. The two “wobble” dimers are significantly more stable than the open dimer formed at O₄, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N₁? H than N₃? H, owing to a more favorable molecular dipole moment alignment when association occurs through H₁. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water–uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.     

Ab initio study of 4-monosubstituted pyrimidines in ground and excited n → π* states

Ab initio SCF and SCF -CI calculations have been performed to investigate substituent effects on ground- and excited-state properties of 4-R-pyrimidines, and to compare these with substituent effects in 2- and 4-R-pyridines, with R including the π donating and σ withdrawing groups CH₃, NH₂, OH, F, and C₂H₃ and the σ and π electron-withdrawing groups CHO and CN. Substitution leads to significant changes in the internal angles of the pyrimidine ring, which are independent of the nature of the substituent. The geometry of the pyrimidine ring is more sensitive to substitution in the 4 position than the pyridine ring geometry is to substitution in either the 2 or the 4 position. The isodesmic reaction energies for substituent transfer from the 4 position of pyrimidine to the 2 or 4 position of pyridine indicate that all R groups except CN have a relative stabilizing effect in pyrimidine. The presence of a π donating group leads to an increase in the n→π* transition energy of 4-R-pyrimidines, while the π withdrawing group CN leads to a decrease in the transition energy relative to pyrimidine. Orbital energy differences and virtual excitation energies tend to correlate with n→π* transition energies of 4-R-pyrimidines with saturated R groups, but such correlations are masked by π conjugation, n orbital interaction, and configurational mixing when the unsaturated groups C₂H₃, CHO, and CN are present. The electronic effects of a π donating group are stronger when the group is bonded to pyrimidine than to pyridine, but those of a π withdrawing group are weaker when the group is bonded to pyrimidine.     

Molecular orbital theory of the hydrogen bond. 26. The hydration of uracil

Ab initio SCF calculations with the STO -3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water–water interactions and nonadditivity effects are also significant.     

Molecular orbital theory of the hydrogen bond. XXX. Water-cytosine complexes

Ab initio SCF and SCF -CI calculations with the STO -3G basis set have been performed to investigate the structures and energies of water–cytosine complexes and the intermolecular water–cytosine surface in the cytosine molecular plane. Although there are six nominal hydrogen-bonding sites in this plane, only three dimers are distinguishable in the ground state. The most stable has an energy of ?10.7 kcal/mol, and is found in the N₁? H and O₂ region. An asymmetric cyclic structure in which the water molecule bridges adjacent N₁? H and O₂ sites is the preferred form of this dimer. The dimer in the region between O₂ and N₄? H′ of the amino group is slightly less stable at ?10.4 kcal/mol, and also has an asymmetric cyclic structure as the preferred structure, with the water molecule bridging amino N₄? H′ and N₃ hydrogen-bonding sites. The third dimer has the amino group as the proton donor to water through the hydrogen cis to C₅, and a stabilization energy of ?7.0 kcal/mol. The water-cytosine surface is characterized by deeper minima and higher barriers than the water-thymine surface and by a decreased mobility of the water molecule between adjacent hydrogen-bonding sites. Absorption of energy by the C₂?O group leads to the first n → π* excited state in which interactions of water with O₂ are broken. The water-cytosine dimers remain bound in this state, but may change structurally. In the second n → π* state interactions between water and N₃ are no longer stabilizing. As a result, the dimer in the O₂ and N₄? H′ region collapses to either a dimer with water the proton donor to O₂, or one with N₄? H′ the proton donor to water. The other two dimers remain bound. All excited dimers are destabilized on vertical excitation relative to the ground state.     

Electronic structure of benzaldehyde: A comparative study of the lowest excited singlet π* ← π and π* ← n states

VE-PPP, CNDO/2, and CNDO/s-CI methods have been used to investigate the electronic spectrum and structure of benzaldehyde. Electronic charge distributions and bond orders in the ground and lowest excited singlet π* ← π and π* ← n states of the molecule have been studied. The molecule has been shown to be nonplanar in the lowest π* ← n excited singlet state, in agreement with the conclusions drawn from the study of vibrational spectra. Dipole moments in both excited states have been shown to be larger than the ground-state value. Thus, the ambiguity in the experimental result for the π* ← π n excited singlet state dipole moment has been resolved. It has been shown that the n orbital is mainly localized on the CHO group. Furthermore, charge distributions, dipole moments, and molecular geometries are shown to be very different in the excited singlet π* ← π and π* ← n states.     

Theoretical study of the π→π* excited states of linear polyenes: The energy gap between 11Bu+ and 21Ag− states and their character

Multireference perturbation theory with complete active space self-consistent field (CASSCF) reference functions is applied to the study of the valence π→π* excited states of 1,3-butadiene, 1,3,5-hexatriene, 1,3,5,7-octatetraene, and 1,3,5,7,9-decapentaene. Our focus was put on determining the nature of the two lowest-lying singlet excited states, 1¹B_u⁺ and 2¹A_g⁻, and their ordering. The 1¹B_u⁺ state is a singly excited state with an ionic nature originating from the HOMO→LUMO one-electron transition while the covalent 2¹A_g⁻ state is the doubly excited state which comes mainly from the (HOMO)²→(LUMO)² transition. The active-space and basis-set effects are taken into account to estimate the excitation energies of larger polyenes. For butadiene, the 1¹B_u⁺ state is calculated to be slightly lower by 0.1 eV than the doubly excited 2¹A_g⁻ state at the ground-state equilibrium geometry. For hexatriene, our calculations predict the two states to be virtually degenerate. Octatetraene is the first polyene for which we predict that the 2¹A_g⁻ state is the lowest excited singlet state at the ground-state geometry. The present theory also indicates that the 2¹A_g⁻ state lies clearly below the 1¹B_u⁺ state in decapentaene with the energy gap of 0.4 eV. The 0–0 transition and the emission energies are also calculated using the planar C_2h relaxed excited-state geometries. The covalent 2¹A_g⁻ state is much more sensitive to the geometry variation than is the ionic 1¹B_u⁺ state, which places the 2¹A_g⁻ state significantly below the 1¹B_u⁺ state at the relaxed geometry. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 157–175, 1998     

Molecular orbital theory of the hydrogen bond.: XVI. A comparative study of pyridine and the diazines as proton acceptors in ground and excited n → π* states

Ab initio LCAO MO SCF calculations with a minimal STO-3G basis set have been performed to determine the structures and energies of dimers having pyridazine, pyrimidine, and pyrazine as proton acceptor molecules, with HF and H₂O as proton donors. The structures of these dimers are consistent with structures anticipated from the General Hybridization Model. Differences in the relative stabilities of dimers in the two series which have HF and H₂O as proton donors and pyridine and the diazines as proton acceptors are attributed to different weightings of secondary effects which influence dimer stabilities. These azabenzeme molecules form stronger hydrogen bonds than HCN and weaker hydrogen bonds than NH₃ whether HF or H₂O is the proton donor. Configuration interaction calculations indicate that vertical excitation to n → π* states of these proton aceptor molecules results in various degrees of destabilization of hydrogen bonded dimers and trimers, depending upon the excited state electron densities at the nitrogen atoms and the excited state dipole moments. With respect to the proton acceptor molecule, computed blue shifts of the n → π* bands increase in the order pyrazine < pyradizine < pyrimidine < pyridine.     

Molecular orbital theory of the hydrogen bond. 27. Substituent effects in water: 4-R-pyrimidine complexes

Ab initio SCF calculations with the STO -3G basis set have been performed to investigate substituent effects on the structures and stabilization energies of water:4-R-pyrimidine complexes, with R including CH₃, NH₂, OH, F, C₂H₃, CHO, and CN. Except for the cyclic water:4-aminopyrimidine complex hydrogen bonded at N₃, these complexes have open structures stabilized by a nearly linear hydrogen bond formed through a nitrogen lone pair of electrons. When hydrogen bonding occurs at N₃, the complexes may have planar or perpendicular conformations depending on the substituent, but when hydrogen bonding occurs at N₁, the perpendicular is generally slightly preferred, and there is essentially free rotation of the 4-R-pyrimidine. Primary substituent effects alter the electronic environment at the nitrogens, and tend to make N₃ a poorer site for hydrogen bonding than N₁, primarily because of a stronger π electron-withdrawing effect at N₃. However, the relative stabilities of complexes hydrogen bonded at N₁ and N₃ are also influenced by secondary substituent effects, which may be significant in stabilizing complexes bonded at N₃. Substitutent effects on the structures and stabilization energies of the water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyridine complexes. Configuration interaction calculations indicate that although absorption of energy by the pyrimidine ring destabilizes the water:4-R-pyrimidine complexes, these may still remain bound in the excited n → π* state. This is in contrast to the fate of open water:2-R-pyridine and water:4-R-pyridine complexes, which dissociate in this state.     

n→π*-Übergänge in Dicarbonylverbindungen Der Einfluss der n,n- und π*, π*-Wechselwirkung

By CNDO-CI calculations we have found that dicarbonyl compounds exhibit only two n → π* transitions in the visible or near UV. region, instead of four as expected from simpler MO-models. The dominant features of the long-wavelength electronic spectra may be characterized by the relative energy of the two n and the two lowest π* orbitals. In general we distinguish between three cases:

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A theoretical study of molecular structure in the excited state and molecular luminescence : III. Types of molecular structure in the excited ππ singlet states

The molecular geometry (bond lengths) in the S₁, and S₂ excited states of a large number of conjugated organic molecules is calculated with the help of the SCF-CI-SC procedure, already described in previous communications. The analysis shows that all excited states studied can be classified in three basic types of structure: (1) with strong conjugation over the whole molecule or along its periphery; (2) with a long main conjugated framework and other shorter conjugated fragments moderately or slightly bonded with the framework and (3) structures consisting of two or more fragments slightly conjugated to each other. An estimation of the role of the possible intramolecular motions of low frequency is done, as well as some other factors contributing to the radiationless deactivation of a given excited state. The presence of structures with both lowest excited singlets of type 1 is shown.