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.     

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.     

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.     

Molecular orbital studies of the NMR hydrogen bond shift

Magnetic shielding constants are calculated for the protons in XOH and XOH…OH₂ (XH, CH₃, NH₂, OH and F) molecules using a slightly extended set of atomic functions modified by gauge factors. These results are used to determine theoretical values for the NMR hydrogen bond shifts in the XOH…OH₂ systems. Such theoretical data are consistent with the few available experimental data. An analysis of the theoretical results reveals that there are three major types of shielding contribution to the NMR hydrogen bond shift; (a) a deshielding change due to the variation of the local currents on the hydrogen bonded proton; (b) a reduction in shielding from currents localized on the oxygen atom of the proton donor; (c) a deshielding contribution from currents induced on the oxygen atom of the proton acceptor. Except for the water dimer, contributions (a), (b) and (c) are of comparable importance for changes in isotropic shielding. For (H₂O)₂ contributions (a) and (c) are somewhat more important than contribution (b). Contribution (c) is almost totally responsible for the changes in the anistropies of the shielding tensors associated with the hydrogen bonded protons. The proton shielding anisotropy changes which occur on hydrogen bond formation are generally much larger than the corresponding variations in the isotropic values of the shielding tensors. This suggests that proton magnetic shielding anisotropies may be more sensitive measures of features of hydrogen bonding than are isotropic proton shielding constants.     

键能的分子轨道理论研究 1: 理论公式

从LCAO-MO出发, 给出了一个计算键能的近似方法, 即EAB(i)-∑∑CaiSabCbiεi为第i个占据分子轨道(MO)中的一对电子对A-B键键能的贡献。对所有分子轨道求和即为该键的键能: EAB=∑EAB(i)。按该方法, 不仅可以计算各种不同分子中每两个相键连原子间的键能, 还可以从MO及AO角度分析每一具体键, 如σ, π, δ键的键能以及各AO对键能的贡献。该方法虽有别于求键焓和平衡离解能De, 但计算结果和De的实验值甚相符合。通过对键能的分析研究, 能较好地揭示原子间的相互作用关系及化学键的强弱, 从而可进一步探讨化学反应活性, 反应速率等化学性质。     

键能的分子轨道理论研究2: 键能与Mulliken布居对键强度的 判断的比较

用键能E~A~B和Mulliken布居对化学键强度的判别进行了分析比较。结果表明,键能判据比Mulliken布居判据所得结论更符合实际情况。作为衡量原子间化学键强度的尺度,不仅应考虑原子轨道间的布居因素,还应考虑分子轨道(或原子轨道)的能量因素。     

Models for the theory of the hydrogen bond: Linear H3/−

An analogy is drawn between the hydrogen bond and the interaction of H₂ with H^– as a prototype. The energy surface for linear H^3/– is calculated using a minimal basis set of 1s orbitals and complete configuration interaction. The appearance of single and double minimum potentials on this surface is discussed.Contribution No. 359 from the Department of Chemistry, Tufts University.     

Localized orbital studies of hydrogen bonding: III. The intramolecular hydrogen bond in 4-methylimino 2-pentanone

Geometry optimizations using the INDO molecular orbital method are carried out on the three possible isomeric forms of 4-methylimino- 2-pentanone. It is found that the molecule strongly prefers a structure containing a hydrogen-bonded chelate ring. Of the two possible isomers containing an intramolecular hydrogen bond, only the structure with the chelated proton closer to the oxygen corresponds to an energy minimum, although the energy surface connecting these two isomers is very flat. The results are interpreted using experimental and calculated NMR properties and energy localized molecular orbitais.     

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. 25. Water–uracil complexes in excited n → π states

Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF -CI calculations on uracil and water–uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C₄? O group, while the second is associated with excitation of the C₂? O group. In the first n → π* state, hydrogen bonds at O₄ are broken, so that the open water–uracil dimer at O₄ dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N₃? H and a cyclic structure at N₃? H and O₄ in the ground state, collapses to a different “wobble” dimer at N₃? H and O₂ in the excited state. The third dimer, a “wobble” dimer at N₁? H and O₂, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O₂ are broken in the second n → π* state, the three water–uracil dimers remain bound. The “wobble” dimer at N₁? H and O₂ changes to an excited open dimer at N₁? H. The “wobble” dimer at N₃? H and O₄ remains intact, and the open dimer at O₄ is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.     

The effect of intramolecular interactions on hydrogen bond acidity

DFT calculations on a range of molecules containing intramolecular hydrogen bonds are reported, with a view to establishing how intramolecular hydrogen bonding affects their intermolecular interactions. It is shown that properties such as the energy of the intramolecular H-bond are unrelated to the ability to form external H-bonds. Conversely, several properties of complexes with a reference base correlate well with an experimental scale of H-bond acidity, and accurate predictive models are determined. A more detailed study, using electrostatic and overlap properties of complexes with a reference base, is used to predict the location, as well as strength, of hydrogen bond acidity. The effects of intramolecular hydrogen bonding on acidity can be seen not just on O-H and N-H, where acidity is greatly reduced, but also on certain C-H groups, which in some cases become the primary source of acidity.     

Molecular orbital studies of hydrogen bonds. IV. Hydrogen bonds in excited states of H2CO with H2O

Ab initio calculations for the interacting system of lower excited states of planar and bent H₂CO with H₂O have been carried out with a minimum basis set, using the recently proposed electron-hole potential method. The blue shifts of the η-π* transition are evaluated as 1100 and 1420 cm^?1 for the singlet and triplet transitions, respectively. In the η-π* states of bent H₂CO, the most stable geometry is one in which an H₂O hydrogen atom is coordinated to the carbon atom.     

Vibrational dynamics of the hydrogen bond in H(2)S-HF: Fourier-transform-infrared spectra and ab initio theory

The rotationally resolved infrared spectrum of the hydrogen bonded complex H(2)S-HF and of its isotopomer D(2)S-DF in the HF/DF stretching range have been observed in a supersonic jet Fourier-transform infrared (FTIR) experiment and indicate a predissociation lifetime of 130 ps for H(2)S-HF. Complementary spectra taken at a temperature of 190 K in a cell without resolved rotational structure indicate the presence of strong anharmonic couplings between low frequency intermolecular modes and the HF donor stretch mode previously observed in other complexes with heavier acceptor molecules without rotational fine structure. The anharmonic analysis of the hot band progressions and of the rotational data confirm the coupling mechanism. The coupling constants and the absolute frequency of the hydrogen bonded stretch mode are in excellent agreement with theoretical predictions based on adiabatic variational calculations on potential surfaces computed at MP2 and CCSD(T) level. Complementary calculations with a perturbational approach further confirm the coupling model.     

Charge transfer theory and vibrational properties of the hydrogen bond

An extension of Mulliken's charge transfer theory leads to the following correlations: the change in the transition moment of the X—H stretching vibration with the enhancement of dipole moment, and the displacement of the X—H stretching frequency with the ionization of donors. Experimental data for a number of hydrogen-bonded complexes are in accord with these predictions.     

Molecular structure of dipivaloylmethane and the intramolecular hydrogen bond problem

Molecular structure of dipivaloylmethane was investigated by X-ray electron diffraction at 24°C. The C_2v and C_s geometrical models involving an intramolecular hydrogen bond are considered. The C_2v model with enol hydrogen lying symmetrically relative to the oxygen atoms has several advantages over the classical model of the enol tautomer. Translated from Zhumal Struktumoi Khimii, Vol. 41, No. 1, pp. 58-66, January–February, 2000