Oxa-bicyclocalixarenes: a new cage for anions via C-H...anion hydrogen bonds and anion...pi interactions

Density functional theory calculations indicate that the cage molecule 4 can trap F- in the gas phase (-80.5 kcal/mol) as well as in CH2Cl2 (-14.7 kcal/mol) via strong C-H...F- hydrogen bonds and pi...F- interaction.     

Weak C-H...O and C-H...F-C hydrogen bonds in the oxirane-trifluoromethane dimer

The oxirane-trifluoromethane dimer generated in a supersonic expansion has been characterized by Fourier transform microwave spectroscopy. The rotational spectra of the parent species and of its two (13)C isotopomers in combination with ab initio calculations have been used to establish a C(s)() geometry for the dimer with the two monomers bound by one C-H.O and two C-H.F-C hydrogen bonds. An overall bonding energy of about 6.7 kJ/mol has been derived from the centrifugal distortion analysis. The lengths of the C-H.O and C-H.F hydrogen bonds, r(O.H) and r(F.H), are 2.37 and 2.68 A, respectively. The C-H.F-C interactions give rise to the HCF(3) internal rotation motion barrier of 0.55(1) kJ/mol, which causes the A-E splittings observed in the rotational spectra. The analysis of the structural and energetic features of the C-H.O and C-H.F-C interactions allows us to classify them as weak hydrogen bonds. Ab initio calculations predict these weak interactions to produce blue shifts in the C-H vibrational frequencies and shortenings of the C-H lengths.     

Limitations of the molecular multipole expansion treatment of electrostatic interactions for C-H...O and O-H...O hydrogen bonds and application of a general charge density approach

A molecular multipole expansion treatment (up to hexadecapole) is examined for its accuracy in describing hydrogen-bond electrostatic interactions, with particular reference to explaining the differences between blue-shifted C-H...O and red-shifted O-H...O bonds. In interactions of H2O and CH4 with point charges at hydrogen-bonding distances, we find that the molecular multipole treatment not only fails to reproduce ab initio energies but also forces on OH or CH bonds, and therefore cannot properly account for the electrostatic component of the interaction. A treatment based on a molecule's permanent charge density and its derivatives and the charge density and its derivatives induced by an external multipole distribution is in full accord with ab initio results, as shown by application to models of the H2O-H2O and CH4-FH systems. Such a charge density approach provides a fundamental basis for understanding the importance of interaction forces in initiating structural change and thereby altering molecular properties.     

C-H...O and other weak hydrogen bonds. From crystal engineering to virtual screening

Hydrogen bonds, X-H...A, formed by weak donors (X = C) and acceptors (A = pi system) were generally dismissed as being of little consequence before and even during the 1970s. This situation changed in the early 1980s, and during the two following decades they were implicated as being significant in many small molecule crystal structures, and also in solution. Today, knowledge gained about these interactions is being used to understand the structure of biomolecules with implications for structure based drug design.     

The C-H...O and C-H...N intramolecular hydrogen bonds in betainealdehydes of azoles containing the pyridinium cation

The comparison of the values of the chemical shifts of the pyridinium protons in the ylides of -dicarbonyl compounds and in betainealdehydes of thiazole and imidazole established the presence of the intramolecular C-H...O and C-H...N hydrogen bond between the -protons of the pyridinium and the oxygen atoms of the formyl group and the nitrogen of the amide fragment in the anionoid part of the betaine. The conclusion was confirmed by the varying influence of the effects of protonation on the character of the deshielding of the - and -protons.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 626–628, May, 1989.     

Intramolecular C-H...Ccarbene hydrogen bonds and competing interactions in monoprotonated tripodal carbenes

The anionic tripodal N-heterocyclic carbene (C3N2H3)3BH- first prepared by Fehlhammer, together with three neutral variants, (C3N2H3)3CH, (C3N2H3)3P, and (C3N2H3)3SiH, have been studied using quantum chemical methods. Isodesmic reactions are used to deduce that the phosphine-bridgehead species in particular has a large-resonance stabilization energy. All the podands undergo substantial conformational change on excitation to the lowest triplet electronic state, with effective localization of the excitation on one of the heterocyclic rings, dearomatizing it. On monoprotonation of the ground states, three of these species display intramolecular C-H...Ccarbene hydrogen bonding: The nature and strength of these interactions is explored using model (intermolecularly hydrogen-bonded) complexes, isodesmic reactions, and GIAO calculations of chemical shifts. One surprising result is that C-H...Ccarbene hydrogen bonds involving ethenic hydrogens can be almost as strong as those involving the imidazolium proton (first identified by Arduengo). The case of the monoprotonated carbon bridgehead species is in particular intriguing. It is stabilized by a competitive Ccarbene...N interaction of sufficient strength to override the C-H...Ccarbene bonding motif observed in the other structures.     

Perturbing the structure of the 2-norbornyl cation through C-H...N and C-H...pi interactions

Quantum chemical studies on complexes of the 2-norbornyl cation with ammonia and benzene are described. These calculations demonstrate that the delocalized, bridged, nonclassical geometry that is usually favored for this carbocation can be perturbed significantly toward the normally less favorable classical geometry through appropriately oriented noncovalent interactions. Since such cations have been proposed as intermediates in enzyme and antibody catalyzed reactions, these results have implications for the nature of the cationic species that may be generated in the presence of electron-rich amino acid side chains of the sort that may be present in the active sites of biocatalysts.     

Influence of N-H...O and C-H...O hydrogen bonds on the 17O NMR tensors in crystalline uracil: computational study

We report a computational study for the 17O NMR tensors (electric field gradient and chemical shielding tensors) in crystalline uracil. We found that N-H...O and C-H...O hydrogen bonds around the uracil molecule in the crystal lattice have quite different influences on the 17O NMR tensors for the two C=O groups. The computed 17O NMR tensors on O4, which is involved in two strong N-H...O hydrogen bonds, show remarkable sensitivity toward the choice of cluster model, whereas the 17O NMR tensors on O2, which is involved in two weak C-H...O hydrogen bonds, show much smaller improvement when the cluster model includes the C-H...O hydrogen bonds. Our results demonstrate that it is important to have accurate hydrogen atom positions in the molecular models used for 17O NMR tensor calculations. In the absence of low-temperature neutron diffraction data, an effective way to generate reliable hydrogen atom positions in the molecular cluster model is to employ partial geometry optimization for hydrogen atom positions using a cluster model that includes all neighboring hydrogen-bonded molecules. Using an optimized seven-molecule model (a total of 84 atoms), we were able to reproduce the experimental 17O NMR tensors to a reasonably good degree of accuracy. However, we also found that the accuracy for the calculated 17O NMR tensors at O2 is not as good as that found for the corresponding tensors at O4. In particular, at the B3LYP/6-311++G(d,p) level of theory, the individual 17O chemical shielding tensor components differ by less than 10 and 30 ppm from the experimental values for O4 and O2, respectively. For the 17O quadrupole coupling constant, the calculated values differ by 0.30 and 0.87 MHz from the experimental values for O4 and O2, respectively.     

Theoretical studies for Lewis acid-base interactions and C-H...O weak hydrogen bonding in various CO2 complexes

Comprehension of the basic concepts for the design of CO2-philic molecules is important due to the possibility for "green" chemistry in supercritical CO2 of substitute solvent systems. Lewis acid-base interactions and C-H...O weak hydrogen bonding were suggested as two key factors in the solubility of CO2-philic molecules. To isolate the stabilization energy of weak hydrogen bonding from the overall binding energy, high-level quantum mechanical calculations were performed for the van der Waals complexes of CO2 with methane, methylacetate, dimethylether, acetaldehyde, and 1,2-dimethoxyethane. Structures and energies were calculated at the MP2 level of theory using the 6-31+G(d) and aug-cc-pVDZ basis sets with basis set superposition error corrections. In addition, the single-point energies were calculated using recently developed multilevel methods. This study shows that the Lewis acid-base interaction has a significant impact on the complex stability compared to the C-H...O weak hydrogen bond. The additional stabilization energy of the cooperative weak hydrogen bond with alpha-proton of the carbonyl group was negligible on the enhancement of supercritical CO2 solubility. However, the stabilization energy was larger for the ether group, such that it may have an important role in increasing the supercritical CO2 solubility. Additional formation of cooperative weak hydrogen bonds may not further increase the solubility due to the stability reduction by steric hindrance.     

Very strong C-H...O, N-H...O, and O-H...O hydrogen bonds involving a cyclic phosphate.

Very short C-H...O, N-H...O, and O-H...O hydrogen bonds have been generated utilizing the cyclic phosphate [CH2(6-t-Bu-4-Me-C6H2O)2]P(O)OH (1). X-ray structures of (i) 1 (unsolvated, two polymorphs), 1...EtOH, and 1...MeOH, (ii) [imidazolium](+)[CH2(6-t-Bu-4-Me-C6H2O)2PO2](-)...MeOH [2], (iii) [HNC5H4-N=N-C5H4NH](2+)[(CH2(6-t-Bu-4-Me-C6H2O)2PO2)2](2-)...4CH3CN...H2O [3], (v) [K, 18-crown-6](+)[(CH2(6-t-Bu-4-Me-C6H2O)2P(O)OH)(CH2(6-t-Bu-4-Me-C6H2O)2PO2)](-)...2THF [4], (vi) 1...cytosine...MeOH [5], (vii) 1...adenine...1/2MeOH [6], and (viii) 1...S-(-)-proline [7] have been determined. The phosphate 1 in both its forms is a hydrogen-bonded dimer with a short O-H...O distance of 2.481(2) [triclinic form] or 2.507(3) A [monoclinic form]. Compound 2 has a helical structure with a very short C-H...O hydrogen bond involving an imidazolyl C-H and methanol in addition to N-H...O hydrogen bonds. A helical motif is also seen in 5. In 3, an extremely short N-H...O hydrogen bond [N...O 2.558(4) A] is observed. Compounds 6 and 7 also exhibit short N-H...O hydrogen bonds. In 1...EtOH, a 12-membered hydrogen-bonded ring motif, with one of the shortest known O-H...O hydrogen bonds [O...O 2.368(4) A], is present. 1...MeOH is a similar dimer with a very short O(-H)...O bond [2.429(3) A]. In 4, the deprotonated phosphate (anion) and the parent acid are held together by a hydrogen bond on one side and a coordinate/covalent bond to potassium on the other; the O-H...O bond is symmetrical and very strong [O...O 2.397(3) A].     

Preparation of the first examples of ansa-spiro substituted fluorophosphazenes and their structural studies: analysis of C-H...F-P weak interactions in substituted fluorophosphazenes

The reactions of fluorophosphazenes, endo ansa FcCH(2)P(S)(CH(2)O)(2)[P(F)N](2)(F(2)PN) (1) (Fc = ferrocenyl) and spiro [RCH(2)P(S)(CH(2)O)(2)PN](F(2)PN)(2) (R = Fc (2), C(6)H(5) (3)], with dilithiated diols have been explored. The study resulted in the formation of the first examples of ansa-spiro substituted fluorinated cyclophosphazenes as well as a bisansa substituted fluorophosphazene. The bisansa compound [1,3-[FcCH(2)P(S)(CH(2)O)(2)]][1,5-[CH(2)(CH(2)O)(2)]]N(3)P(3)F(2) (4) was found to be nongeminaly substituted with both the ansa rings in cis configuration, which is in stark contrast to the observations on cyclic chlorophosphazenes where geminal bisansa formation has been observed. The ansa-spiro compounds (5-7) underwent the ansa to spiro transformation leading to dispiro compounds in the presence of catalytic amounts of CsF at room temperature. Two of the ansa-spiro compounds, endo-[3,5-[FcCH(2)P(S)(CH(2)O)(2)]][1,1-[CH(2)(CH(2)O)(2)]]N(3)P(3)F(2) (5) and endo-[3,5-[FcCH(2)P(S)(CH(2)O)(2)]][1,1-[FcCH(2)P(S)(CH(2)O)(2)]]N(3)P(3)F(2) (6), were structurally characterized, and the crystal structures indicate boat-chair conformation as well as crown conformation for the eight-membered ansa rings. Weak C-H.F-P interactions observed in the crystal structures of the ansa-spiro substituted fluorophosphazene derivatives have been analyzed and compared with C-H.F-P interactions of other fluorinated phosphazenes and thionyl phosphazenes.     

Parallel sheet structure in cyclopropane gamma-peptides stabilized by C-H...O hydrogen bonds

A three-residue trans-cyclopropane gamma-peptide adopts an infinite parallel sheet structure in the solid state stabilized by intermolecular C-H...O hydrogen bonds, as demonstrated by single crystal X-ray diffraction.     

High-pressure Raman studies on aqueous protonated thiazole: presence of charge-enhanced C-H...O hydrogen bonds

Close interactions of the charge-enhanced C-H...O type have been analyzed both experimentally and computationally in the protonated thiazole-water system. The formation of a weak hydrogen bond was directly evidenced by a low-frequency shift of the hydrogen-bonded aromatic C-H stretch in the protonated thiazole moiety. For pure thiazole, the pressure dependence of the C-H bands yielded blue frequency shifts. The peak frequency of the aromatic C-H stretch band of protonated thiazole in a dilute D2O solution possesses an unusual nonmonotonic pressure dependence, which indicates enhanced C-H...O hydrogen-bond formation at high pressure. We performed density functional theory calculations to predict the frequency shift of the C-H stretching vibrations. The reorganization of the hydrogen-bonded network may be one of the factors to induce the blue frequency shift to the red frequency shift.     

Binding of an acetonitrile molecule inside the ethereal cavity of a hexaarylbenzene-based receptor via a synergy of C-H...O/C-H...pi interactions

A pair of hexaarylbenzene-based receptors, which contain a circular, as well as a partially-broken, ethereal fence around the central benzene ring, bind acetonitrile molecules via a synergy of C-H...O and C-H...pi interactions, as probed by X-ray crystallography.     

Multicoefficient extrapolated density functional theory studies of pi...pi interactions: the benzene dimer

We report tests of new (2005) and established (1999-2003) multilevel methods against essentially converged benchmark results for nonbonded interactions in benzene dimers. We found that the newly developed multicoefficient extrapolated density functional theory (DFT) methods (which combine DFT with correlated wave function methods) give better performance than multilevel methods such as G3SX, G3SX(MP3), and CBS-QB3 that are based purely on wave function theory (WFT); furthermore, they have a lower computational cost. We conclude that our empirical approach for combining WFT methods with DFT methods is a very efficient and effective way for describing not only covalent interactions (as shown previously) but also nonbonded interactions.     

Solution phase measurement of both weak sigma and C-H...X- hydrogen bonding interactions in synthetic anion receptors

A series of tripodal receptors preorganize electron-deficient aromatic rings to bind halides in organic solvents using weak sigma anion-to-arene interactions or C-H...X- hydrogen bonds. 1H NMR spectroscopy proves to be a powerful technique for quantifying binding in solution and determining the interaction motifs, even in cases of weak binding.