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. 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.     

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.     

Ground-state properties of benzenoid hydrocarbons by simple bond orbital resonance theory approach

π-electron energies and bond orders of benzenoid hydrocarbons with up to five fused hexagons have been considered by the simple Bond Orbital Resonance Theory (BORT) approach. The corresponding ground states were determined according to four BORT models. In the first three models a diagonalisation of the Hückel-type Hamiltonian was performed in the bases of Kekulé, of Kekulé and mono-Claus and of Kekulé and Claus resonance structures, respectively. In the fourth model a simple BORT ansatz was used. According to this ansatz, the ground state is a linear combination of the positive Kekulé structures, all with equal coefficients. It was shown that π-electron energies and bond orders obtained by these models correlate much better with the PPP energies and bond orders than with the Hückel energies and bond orders. This indicates that a simple BORT approach is quite reliable in predicting the more sophisticated PPP results. Concerning the relative performance of the four BORT models, the best results were obtained with the BORT ansatz. The performance deteriorates with the expansion of the basis set. This is attributed to the fact that in these models the improvement of the basis set is not accompanied with the corresponding improvement of the Hamiltonian. Comparing the BORT-ansatz bond orders with the Pauling bond orders, it was shown that BORT-ansatz bond orders correlate much better with the PPP bond orders. This revised version was published online in July 2006 with corrections to the Cover Date.     

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.     

Molecular orbital theory of electron donor-acceptor complexes

A Gaussian basis set consisting of 12s-type, 6p-type and 4d-type functions has been optimized for the third row atoms, together with a 9s, 5p, 3d set for the corresponding dipositive ion. The applicability of these atomic sets for molecular calculation is discussed.

---

Zusammenfassung Ein Basissatz von 12s-, 6p- und 4d-Funktionen für die Atome der dritten Reihe des periodischen Systems ist optimalisiert worden; das gleiche gilt für einen entsprechenden Satz für die zweifach positiven Ionen aus 9s-, 5p- und 3d-Funktionen. Ferner wird ihre Anwendbarkeit bei Rechnungen an Molekülen diskutiert.

---

Résumé On présente un ensemble optimal de fonctions de base gaussiennes pour les atomes et les ions de la troisième ligne. Cet ensemble est constitué de 12 fonctions du type s, 6 fonctions du type p et 4 fonctions du type d pour l'atome neutre et de 9 fonctions s, 5 fonctions p et 3 fonctions d pour l'ion M²⁺. On discute l'emploi de ces bases pour des calculs moléculaires.

     

Relative strength of hydrogen bond interaction in alcohol–water complexes

Hydrogen binding energies are calculated for the different isomers of 1:1 complexes of methanol, ethanol and water using ab initio methods from MP2 to CCSD(T). Zero-point energy vibration and counterpoise corrections are considered and electron correlation effects are analyzed. In methanol–water and ethanol–water the most stable heterodimer is the one where the water plays the role of proton donor. In methanol–ethanol the two isomers have essentially the same energy and no favorite heterodimer could be discerned. The interplay between the relative binding energy is briefly discussed in conjunction with the incomplete mixing of alcohol–water systems.     

Molecular orbital theory of the hydrogen bond : XXXII. The effect of H and Li association on the A---T and G---C pairs

Ab initio molecular orbital calculations have been performed to determine the structures and stabilization energies of the A---T and G---C base pairs and their complexes with H⁺ and Li⁺, H⁺ and Li⁺ association stabilizes the A---T pair except for Li⁺ association at O₄ in thymine. Protonation of thymine stabilizes the A---T pair to a greater extent than protonation of adenine. The association of H⁺ and Li⁺ with guanine stabilizes the G---C pair, but protonation of cytosine destabilizes G---C. Changes in the structures of the hydrogen bonds in the A---T and G---C pairs reflect changes in hydrogen bond strengths.     

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。     

Molecular orbital studies of hydrogen bonds

The ground state, the lowest singlet and triplet n-* states, and the lowest triplet -* state of the formic acid monomer and dimer are studied with the ab initio molecular orbital theory. The two-configuration electron-hole potential method is used for calculations of excited states of dimers. The potential energy curves for the symmetrical simultaneous movement of two bridging protons are studied for all of the states. The barrier of the proton transfer in the ground state is found to be the smallest of the states studied. The association energy is analyzed in terms of various components.A preliminary account has been presented at the First International Congress of Quantum Chemistry, Menton, France, 1973, and has appeared in Ref. [3].     

Comparative analysis of blue‐shifted hydrogen bond versus conventional hydrogen bond in methyl radical complexes

Methyl radical complexes H₃C…HCN and H₃C…HNC have been investigated at the UMP2(full)/aug‐cc‐pVTZ level to elucidate the nature of hydrogen bonds. To better understand the intermolecular H‐bond interactions, topological analysis of electron density at bond critical points (BCP) is executed using Bader's atoms‐in‐molecules (AIM) theory. Natural bond orbital (NBO) analysis has also been performed to study the orbital interactions and change of hybridization. Theoretical calculations show that there is no essential difference between the blue‐shift H‐bond and the conventional one. In H₃C…HNC complex, rehybridization is responsible for shortening of the N? H bond. The hyperconjugative interaction between the single electron of the methyl radical and N? H antibonding orbital is up to 7.0 kcal/mol, exceeding 3.0 kcal/mol, the upper limit of hyperconjugative n(Y)→σ*(X–H) interaction to form the blue‐shifted H‐bond according to Alabugin's theory. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Charge-transfer properties of the hydrogen bond: Part 6. Charge-transfer theory and dipole moments of hydrogen-bonded complexes

The enhancement of the dipole moments of hydrogen-bonded complexes are discussed using Mulliken's charge-transfer theory.A linear relation is found between the ratio a/b and the ionization potential of the donor, I^V_D. This behaviour is similar to that previously found for halogen charge-transfer complexes [6].     

Transitions of the hydrogen bond in epoxy–diamine networks

The variation of the fundamental hydroxyl stretching frequency in the infrared spectrum of a number of epoxy–diamine networks has been determined as a function of temperature. Short-range hydrogen bonds appear to be formed in all the epoxy networks examined. For polymers formed by using short-chain α,ω-diamines, it appears that a hydroxyl–hydroxyl bond is dominant. For longer chain lenghts, a hydroxylamine bond becomes important. The hydroxyl–hydroxyl bond breaks at the glass transition temperature, whereas the hydroxyl–amine bond breaks at a higher temperature. At the highest temperatures studied, all hydroxyl groups form weak short-range bonds to the alkyl-aryl ether function. The absorption frequency for the hydroxyl group in all types of hydrogen bonds formed shows a strong dependence on temperature and absorption moves to a higher wavenumber with increase in temperature.     

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。     

Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes.

The benzene...X complexes (X=benzene, antracene, ovalene) were optimised at the MP2/6-31G** level with the C2v symmetry of the complex and planarity of the proton acceptor being preserved. The resulting stabilisation energies amount to 1.2, 2.3 and 2.9 kcal mol(-1), and the C-H bond of the proton donor is contracted by 0.0035, 0.0052 and 0.0055 A, respectively. The contraction is connected with a blue-shift of the C-H stretch vibration frequency. A two-dimensional anharmonic vibration treatment based on a MP2/6-31G** potential energy surface yields the following blue shifts for the complexes studied: 28, 42 and 43 cm(-1). The dominant attraction in the complexes is London dispersion, while the attractive contribution from electrostatic quadrupole-quadrupole interactions is considerably smaller.     

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.     

A molecular orbital explanation of bond distance variation caused by hydrogen bond formation

For hydrogen bond systems X–D–HA–Y, a simple molecular orbital model is proposed to understand the mechanism of the bond distance variations caused by the hydrogen bond formation. This model explains the bond distance variations for X–D and A–Y as follows. Electrostatic potential that the electrons in a molecule receive from other molecules causes the changes in atomic orbital energy differences between the bonded atoms. Then, the changes in the orbital energy differences make the bond orders larger or smaller and consequently the bond distances vary. The validity of this model has been confirmed by the effective fragment potential method, using the test systems of (HCOOH)₂, HCONH₂ (formamide) crystal and BF₃·2H₂O crystal.     

Molecular orbital calculations of bond lengths in benzenoid hydrocarbons

The correlation between bond lengths and bond orders in benzenoid hydrocarbons has been considered. Bond orders for six molecules were obtained by means of a simple MO-LCAO-SC treatment, and a procedure is suggested for calculating accurate bond lengths from such self-consistent bond orders.