Molecular beam rotational spectrum of cyclobutanone-trifluoromethane: nature of weak CH...O=C and CH...F hydrogen bonds

The molecular beam Fourier transform microwave spectrum of cyclobutanone-trifluoromethane has been assigned and measured. The carbon atom of trifluoromethane lies in the plane of the heavy atoms of cyclobutanone. The complex is stabilized by one C-H...O=C and two C-H...F-C weak hydrogen bonds. The C-H...O=C interaction, involving one carbonylic oxygen, is studied for the first time in detail with rotationally resolved spectroscopy. The two C-H...F-C weak hydrogen bonds involve two fluorine atoms of trifluoromethane and two hydrogens of the same methylenic group in the alpha position.     

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.     

Cooperativity between OH...O and CH...O hydrogen bonds involving dimethyl sulfoxide-H2O-H2O complex

The cooperativity between the O-H...O and C-H...O hydrogen bonds has been studied by quantum chemical calculations at the MP2/6-311++G(d,p) level in gaseous phase and at the B3LYP/6-311++G(d,p) level in solution. The interaction energies of the O-H...O and C-H...O H-bonds are increased by 53 and 58%, respectively, demonstrating that there is a large cooperativity. Analysis of hydrogen-bonding lengths, OH bond lengths, and OH stretching frequencies also supports such a conclusion. By NBO analysis, it is found that orbital interaction plays a great role in enhancing their cooperativity. The strength increase of the C-H...O H-bond is larger than that of the O-H...O H-bond due to the cooperativity. The solvent has a weakening effect on the cooperativity.     

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].     

Blue-shifting intramolecular C-H...O interactions

Two model systems, 3-methylacroleine and 3-(difluoromethyl)acroleine, are investigated computationally with respect to the character of the C-H...O interaction in their chelate-type (ZZ) conformers. By selecting the appropriate reference conformers, the C-H...O interaction is shown to result in the increase of the C-H stretching frequency (i.e., in the blue shift of the C-H stretching band). This is accompanied by the shortening of the C-H bond distance as compared to its values in reference molecules. Parallel to calculations of the C-H bond distance and stretching frequency, the energy contribution of the C-H...O interaction to the total energy (i.e., the energy associated with the C-H...O contact) is evaluated by using the methods proposed recently for the estimation of the energies of intramolecular hydrogen bonds. It is found that the C-H...O contact in the chelate-type forms of 3-methylacroleine and 3-(difluoromethyl)acroleine corresponds to the negative energy contribution and is repulsive. It is concluded that, despite the stability of the ZZ conformers of the two molecules and their deceptive structural shape, no hydrogen bond in the usual sense is formed between the C-H bond and the lone pair donor. The results are interpreted in terms of the steric compression, which leads to the dominance of the valence repulsion contribution in the C-H...O contact. This mechanism suggests that blue-shifting intramolecular interactions should not be that uncommon, although their recognition requires a careful consideration of the reference system.     

Exploring the lower limit in hydrogen bonds: analysis of weak C-H...O and C-H...pi interactions in substituted coumarins from charge density analysis

Experimental electron densities in coumarin, 1-thiocoumarin, and 3-acetylcoumarin have been analyzed based on the X-ray diffraction data at 90 K. These compounds pack in the crystal lattice with weak C-H...O and C-H...pi interactions, and variations in charge density properties and derived local energy densities have been investigated in the regions of intermolecular interactions. Theoretical charge density calculations on crystals using the B3LYP/6-31G* method show remarkable agreement with the derived properties and energy densities from the experiment. The intermolecular interactions follow an exponential dependence of electron density and energy densities at the bond critical points. The Laplacian follows a "Morse-like" dependence on the length of the interaction line. Based on the set of criteria defined using the theory of "atoms in molecules", it has become possible to distinguish between a hydrogen bond (C-H...O) and a van der Waals interaction (C-H...pi). This has resulted in the identification of a "region of overlap" in terms of electron densities, energy densities, and mutual penetration of the hydrogen and acceptor atoms with respect to the interaction length. This approach suggests a possible tool to distinguish between the two types of interactions.     

Hydrogen bond stabilization in 1,3-dimethylimidazolium methyl sulfate and 1-butyl-3-methylimidazolium hexafluorophosphate probed by high pressure: the role of charge-enhanced C-H...O interactions in the room-temperature ionic liquid

The hydrogen bonding structures of room-temperature ionic liquids 1,3-dimethylimidazolium methyl sulfate and 1-butyl-3-methylimidazolium hexafluorophosphate have been studied by infrared spectroscopy. High-pressure infrared spectral profiles and theoretical calculations allow us to make a vibrational assignment of these compounds. The imidazolium C-H bands of 1,3-dimethylimidazolium methyl sulfate display anomalous non-monotonic pressure-induced frequency shifts. This discontinuity in frequency shift is related to enhanced C-H...O hydrogen bonding. This behavior is in contrast with the trend of blue shifts in frequency for the methyl C-H stretching mode at ca. 2960 cm(-1). Our results indicated that the imidazolium C-H groups are more favorable sites for hydrogen bonding than the methyl C-H groups in the pure 1,3-dimethylimidazolium methyl sulfate. Nevertheless, both methyl C-H and imidazolium C-H groups are favorable sites for C-H...O hydrogen bonding in a dilute 1,3-dimethylimidazolium methyl sulfate/D(2)O mixture. Hydrogen bond-like C-H...F interactions were observed between PF(6)(-) and H atoms on the alkyl side chains and imidazolium ring for 1-butyl-3-methylimidazolium hexafluorophosphate.     

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.     

An investigation of weak CH...O hydrogen bonds in maltose anomers by a combination of calculation and experimental solid-state NMR spectroscopy

Two-dimensional (1)H-(13)C MAS-J-HMQC solid-state NMR spectra of the two anomeric forms of maltose at natural abundance are presented. The experimental (1)H chemical shifts of the CH and CH(2) protons are assigned using first-principles chemical shift calculations that employ a plane-wave pseudopotential approach. Further calculations show that the calculated change in the (1)H chemical shift when comparing the full crystal and an isolated molecule is a quantitative measure of intermolecular C-H...O weak hydrogen bonding. Notably, a clear correlation between a large chemical shift change (up to 2 ppm) and both a short H...O distance (<2.7 A) and a CHO bond angle greater than 130 degrees is observed, thus showing that directionality is important in C-H...O hydrogen bonding.     

Weak, improper, C-O...H-C hydrogen bonds in the dimethyl ether dimer

The ground-state rotational spectrum of the dimethyl ether dimer, (DME)(2), has been studied by molecular beam Fourier transform microwave and free jet millimeter wave absorption spectroscopies. The molecular beam Fourier transform microwave spectra of the (DME-d(6))(2), (DME-(13)C)(2), (DME-d(6))...(DME), (DME-(13)C)...(DME), and (DME)...(DME-(13)C) isotopomers have also been assigned. The rotational parameters have been interpreted in terms of a C(s) geometry with the two monomers bound by three weak C-H...O hydrogen bonds, each with an average interaction energy of about 1.9 kJ/mol. The experimental data combined with high-level ab initio calculations show this kind of interaction to be improper, blue-shifted hydrogen bonding, with an average shortening of the C-H bonds involved in the hydrogen bonding of 0.0014 A. The length of the C-H...O hydrogen bonds, r(O...H), is in the range 2.52-2.59 A.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

Steric effect on construction of extended architectures of Ni(II) complexes directed by intermolecular C-H...F and C-H...O interactions

Five new Ni(II) complexes with pyridine carboxamide ligands have been synthesized and the crystal structures of three of the complexes were determined. Strong distortion effects of 6-methyl substitution were observed in the complexes with 6-methyl-substituted pyridyl bpb ligands. The C-H...F and C-H...O hydrogen bond interactions build extended architectures in the crystals studied. This result suggests that the steric effect of 6-methyl substitution plays an important role in the distortion of the structure, and the 6-methyl substitution can facilitate hydrogen bond interactions between methyl hydrogen atoms and O(carbonyl) or F atoms. Twelve Ni(II) complexes, including seven complexes reported previously, show reversible redox behavior, implying that the reduced Ni(I) state of each complex is stable in the time scale of CV measurement. The steric effect of R₁ substituent and the electronic effects of X₁ and X₂ groups were found to be the main factors contributing to the shift of the redox potential of the Ni(II) complexes     

Tailoring the key in a molecular lock-and-key model system: the propylene oxide...2-fluoroethanol complex

The conformational isomerism of the propylene oxide (PO)...2-fluoroethanol (FE) complex has been investigated using molecular beam Fourier-transform microwave spectroscopy complemented with high level ab initio calculations. Rotational transitions of three different binary conformers have been observed experimentally. On the basis of the agreement of the experimental and calculated rotational constants, they could be identified as the three most stable structures, anti G-g+, anti G+g-, and syn G+g-. All the observed structures exhibit a primary O-H...O hydrogen bond, an intramolecular O-H...F hydrogen bond and two secondary intermolecular C-H...F contacts. The two anti conformers, with FE and the PO methyl group on the opposite sides of the oxirane ring, show higher abundances than the syn conformer. In all three observed conformers, FE remains approximately in its favorable compact gauche conformation. The monofluorination of the molecular lock-and-key model system PO...ethanol increases not only the number of possible binary conformers, but also the discrimination energy among them. The superior discrimination ability of FE as compared to ethanol classifies it as a tailored key to the PO lock.     

How to determine whether intramolecular H...H interactions can be classified as dihydrogen bonds

Different types of intramolecular H...H interactions have been analyzed using the MP2/6-311++G(d,p) level of approximation. These are C-H...H-B, C-H...H-Al, C-H...H-C, C-H...H-O, O-H...H-Al and O-H...H-B contacts. Quantum theory of atoms in molecules and natural bond orbitals methods were applied to better understand the nature of these interactions. It was found that some of the species analyzed possess the characteristics of typical hydrogen bonds, such as the O-H...O ones. The electron charge transfer from the Lewis base to the antibonding X-H (for example O-H) orbital of the Lewis acid is one such characteristic. The NBO method may be considered decisive to classify any system as dihydrogen bonded.     

Interplay of phenyl-perfluorophenyl stacking,C-H...F,C-F...pi and F...F interactions in some crystalline aromatic azines

Analysis of phenyl-perfluorophenyl stacking synthon, C-H...F, C-F...pi interactions, and F...F tetramer in three closely related azine crystal structures shows the dominance of Ar-ArF synthon while other interactions are turned on/off depending on the H/F stoichiometry in the molecule.     

C-H Group as proton donor by formation of a weak hydrogen bond

A systematic CNDO/2 study has been carried out on the weak C-H...F, C-H...O, and C-H...N hydrogen bonds. An H-bond formation has been revealed for proton donors with negative excess charge on the hydrogen. The concept of the positive character of the hydrogen as well as some essential features of the hydrogen bond have been discussed. Some useful correlations have been found and the importance of the charge shifts has been emphasized.     

Contributions of NH...O and CH...O hydrogen bonds to the stability of beta-sheets in proteins

Ab initio quantum calculations are applied to both the parallel and the antiparallel arrangements of the beta-sheets of proteins. The energies of the NH...O and CH...O hydrogen bonds present in the beta-sheet are evaluated separately from one another by appropriate modifications of the model systems. The bond energies of these two sorts of hydrogen bonds are found to be very nearly equal in the parallel beta-sheet. The NH...O bonds are stronger than CH...O in the antiparallel geometry but only by a relatively small margin. Moreover, the former NH...O bonds are weakened when placed next to one another, as occurs in the antiparallel beta-sheet. As a result, there is little energetic distinction between the NH...O and CH...O bonds in the full antiparallel beta-sheet, just as in the parallel structure.     

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.     

C-H...N and C-H...S hydrogen bonds--influence of hybridization on their strength

Simple complexes connected through C-H...S and C-H...N interactions are investigated: CH4...NH3, C2H4...NH3, C2H2...NH3, CH4...SH2, C2H4...SH2, and C2H2...SH2. Ab initio and DFT calculations are performed (SCF, MP2, B3LYP) using different basis sets up to the MP2/aug-cc-pVQZ//MP2/aug-cc-pVDZ level of approximation. The Bader theory is applied since MP2/6-311++G(d,p) wave functions are used to find and to characterize bond critical points in terms of electron densities and their Laplacians. The influence of hybridization on the properties of C-H...S and C-H...N systems is also studied showing that the strength of such interactions increases in the following order: C(sp3)-H...Y, C(sp2)-H...Y, C(sp)-H...Y, where Y = S, N--it is in line with the previous findings on C-H...O hydrogen bonds. The results also show that CH4...SH2 and C2H4...SH2 complexes should be rather classified as van der Waals interactions and not as hydrogen bonds. The frequency associated with the C-H stretch of C(sp3)-H...S is blue-shifted.     

Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding by matrix-isolation infrared spectroscopy

Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding is presented. Argon matrix-isolation infrared spectra of 1-methoxy-2-(dimethylamino)ethane exhibit a band at 3016.5 cm-1. Spectral behavior with annealing indicates that this band is assigned to the most stable conformer, trans-gauche-(trans|gauche'), with an intramolecular C-H...O hydrogen bond. Density functional calculations show that this band arises from the stretching vibration of the C-H bond participating in the formation of the C-H...O hydrogen bond. The C-H bond is shortened by 0.004 A, and the C-H stretching band is blue-shifted by at least 35 cm-1 on the formation of the hydrogen bond. The (C)H...O distance is calculated as 2.38 A, which is shorter than the corresponding van der Waals separation by 0.3 A.