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.     

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.     

Transformations of griseofulvin in strong acidic conditions--crystal structures of 2'-demethylgriseofulvin and dimerized griseofulvin

The structure of griseofulvic acid, C16H15ClO6, at 100 K has orthorhombic (P2(1)2(1)2) symmetry. It is of interest with respect to biological activity. The structure displays intermolecular O-H...O, C-H...O hydrogen bonding as well as week C-H...pi and pi...pi interactions. In strong acidic conditions the griseofulvin undergoes dimerization. The structure of dimerized griseofulvin, C34H32C12O12 x C2H6O x H2O, at 100 K has monoclinic (P2(1)) symmetry. The molecule crystallized as a solvate with one ethanol and one water molecule. The dimeric molecules form intermolecular O-H...O hydrogen bonds to solvents molecules only but they interact via week C-H...O, C-H...pi, C-Cl...pi and pi...pi interactions with other dimerized molecules.     

Supramolecular assemblies of a bis(terpyridine) ligand and of its [2x2] grid-type Zn(II) and Co(II) complexes on highly ordered pyrolytic graphite

The synthesis and characterisation of bis(terpyridine)-derived ligands which are capable of forming [2x2] grid-like complexes is presented. Additional pyridine substituents on these ligands do not interfere with the complexation process. Adsorbing one of the pure ligands on highly ordered pyrolytic graphite (HOPG) shows a highly ordered structure stabilised by additional weak intermolecular C-H...N hydrogen bonds partially through the extra-pyridines as could be shown by scanning tunneling microscopy (STM) investigations. Similar adsorption experiments with one of the corresponding [2x2] Co(II) grid-type complexes on graphite, led also to a well-organised structure with interdigitation of the extra-pyridine moieties.     

Strongly blue-shifted C-H stretches: interaction of formaldehyde with hydrogen fluoride clusters

The equilibrium structures, binding energies, and vibrational spectra of the cyclic, hydrogen-bonded complexes formed between formaldehyde, H(2)CO, and hydrogen fluoride clusters, (HF)(1< or =n < or =4), are investigated by means of large-scale second-order M?ller-Plesset calculations with extended basis sets. All studied complexes exhibit marked blue shifts of the C-H stretching frequencies, exceeding 100 cm(-1) for n = 2-4. It is shown that these blue shifts are, however, only to a minor part caused by blue-shifting hydrogen bonding via C-H...F contacts. The major part arises due to the structural relaxation of the H(2)CO molecule under the formation of a strong C=O...H-F hydrogen bond which strengthens as n increases. The close correlation between the different structural parameters in the studied series of complexes is demonstrated, and the consequences for the frequency shifts in the complexes are pointed out, corroborating thus the suggestion of the primary role of the C=O...H-F hydrogen bonding for the C-H stretching frequency shifts. This particular behavior, that the appearance of an increasingly stronger blue shift of the C-H stretching frequencies is mainly induced by the formation of a progressively stronger C=O...H-F hydrogen bond in the series of H(2)CO...(HF)(1< or =n < or =4), complexes and only to a lesser degree by the formation of the so-called blue-shifting C-H...F hydrogen bond, is rationalized with the aid of selected sections of the intramolecular H(2)CO potential energy surface and by performing a variety of structural optimizations of the H(2)CO molecule embedded in external, differently oriented dipole electric fields, and also by invoking a simple analytical force-field model.     

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.     

Hydration-induced changes of structure and vibrational frequencies of methylphosphocholine studied as a model of biomembrane lipids

The chemical characteristics of the polar parts of phospholipids as the main components of biological membranes were investigated by using infrared (IR) spectroscopy and theoretical calculations with water as a probe molecule. The logical key molecule used in this study is methylphosphocholine (MePC) as it is not only a representative model for a polar lipid headgroup but itself has biological significance. Isolated MePC forms a compact (folded) structure which is essentially stabilized by two intramolecular C-H...O type hydrogen bonds. At lower hydration, considerable wavenumber shifts were revealed by IR spectroscopy: the frequencies of the (O-P-O)- stretches were strongly redshifted, whereas methyl and methylene C-H and O-P-O stretches shifted surprisingly to blue. The origin of both red- and blueshifts was rationalized, on the basis of molecular-dynamics and quantum-chemistry calculations. In more detail, the hydration-induced blueshifts of C-H stretches could be shown to arise from several origins: disruption of the intramolecular C-H...O hydrogen bonds, formation of intermolecular C-H...O(water) H-bonds. The stepwise disruption of the intramolecular hydrogen bonds appeared to be the main feature that causes partial unfolding of the compact structure. However, the transition from a folded to extended MePC structure was completed only at high hydration. One might hypothesize that the mechanism of hydration-driven conformational changes as described here for MePC could be transferred to other zwitterions with relevant internal C-H...O hydrogen bonds.     

The sticking of H and D atoms on a graphite (0001) surface: the effects of coverage and energy dissipation

Classical trajectory methods are used to examine the trapping and sticking of H and D atoms on the graphite (0001) surface. Total energy calculations based on density functional theory are used to construct the model potential energy surface, and graphite clusters of up to 121 atoms are considered. For hydrogen to chemisorb, the bonding carbon must pucker out of the surface plane by roughly 0.4 A. For incident energies above the 0.2 eV barrier, any trapped H atoms must rapidly dissipate their excess energy into the surrounding lattice within a few vibrations of the C-H stretch in order to remain bound. For sufficiently large clusters, the C-H bond stabilizes within about 0.1 ps. The sticking probability for D at 150 K is in the range of 5%-10%, more-or-less consistent with the most recent measurements in the limit of zero coverge. Variation with isotope and substrate temperature is weak. We estimate that the sticking cross section for adsorption at the para site, directly across the sixfold carbon ring from an already adsorbed H atom, can be four or more times larger that the zero coverage sticking cross section.     

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.     

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.     

Synthesis and structural studies of 1,1'-bis-amino-functionalized ferrocenes, ferrocene salts, and ferrocenium salts

Having isolated and characterized a series of sodium cyclopentadienide salts, we have synthesized a number of 1,1'-bis-amino-functionalized ferrocenes, 1,1'-bis-amino-functionalized ferrocene salts, and 1,1'-bis-amino-functionalized ferrocenium salts. Among these are the first crystallographically characterized examples of cyclopentadienyl units containing (piperidin-N-ylethyl)- and (pyrid-2-ylmethyl)cyclopentadienyl side chains. In the cases of some of the ferrocenes, ferrocene salts, and ferrocenium salts, there are some interesting structural features in the solid state. These include C-H...N and C-H...pi cloud interactions as well as N-H...O and N-H...F hydrogen bonds.     

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.     

Comparative study of weak interactions in molecular crystals: H-H bonds vs hydrogen bonds

The crystal structures of tetraphenylphosphonium squarate, bianthrone, and bis(benzophenone)azine are shown to contain a variety of C-H(delta+)...(delta+)H-C interactions, as well as a variety of C-H...O and C-H...C(pi) interactions. Each of these molecules possesses interactions that can possibly be characterized as either H-H bonds or weak hydrogen bonds based on the first four criteria proposed by Koch and Popelier. These interactions have been completely characterized topologically after the multipole refinement of the structures. It appears that weak interactions of the form C-H(delta+)...(delta+)H-C possess certain correlations between the various properties of the electron density at the bond critical points. The coexistence of the three types of interactions makes it possible to establish similarities and differences in the correlations of these weak interactions. This all leads to a better understanding of H-H interactions and how they fit into the hierarchy of weak interactions.     

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.     

不同温度处理的糠醇和聚苯胺树脂碳化产物结构基因变化的红外光谱研究

红外光谱测试结果表明糖醇树脂碳化过程中五员杂环上的碳氧键首先发生断裂,使氧脱出,而剩余的双烯链状结构再进行重排,形成六员稠环结构,并在此基础上发生脱氢反应生成石墨微晶。测试结果还表明聚苯胺树脂中的氮在碳化过程中的稳定性与其相连结的基团结构有密切关系。苯环相连的氮比与苯酚基相连的氮具有更强的抗热解稳定性。聚苯胺碳化产物中的氢主要分为两大类：一类是以碳氢键的形式存在;另一类则是以氮氢键的形式存在。碳化产物中的氢主要是在苯的稠环结构上以碳氢键形式存在。     

Theoretical investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes

Systematic investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes has revealed that fluorobenzene, difluorobenzene, and trifluorobenzene favor formation of cyclic complexes with a C-H...N-H...F-C binding motif. On the other hand, tetrafluorobenzene and pentafluorobenzene favor formation of linear C-H...N hydrogen-bonded complexes. The complete absence of exclusively linear N-H...F hydrogen-bonded complexes for the entire series indicates that C-F bond in fluorobenzenes is a reluctant hydrogen-bond acceptor. However, fluorine does hydrogen bond when cooperatively stabilized with C-H...N hydrogen bonds for the lower fluoro analogues. The propensity of fluorobenzenes to adapt to the C-H...N-H...F-C binding motif decreases with the progressive fluorination of the benzene ring and disappears completely when benzene ring is substituted with five or more fluorine atoms.     

Structure and matrix isolation infrared spectrum of formyl fluoride dimer: blue-shift of the C-H stretching frequency

Infrared spectroscopy (IR) of formyl fluoride (HCOF) dimer is studied in low-temperature argon and krypton matrixes. New IR absorptions, ca. 17 cm(-1) blue shifted from the monomer C-H stretching fundamental, are assigned to the HCOF dimer. The MP2/6-311++G calculations were utilized to define structures and harmonic frequencies of various HCOF dimers. Among the four optimized structures, the dimer having two C-H...O hydrogen bonds possesses strongest intermolecular bonding. The calculated harmonic frequencies of this dimer structure are shifted from the monomer similarly as observed in the experiment. Thus, we suggest that the experimentally observed blue shifted C-H bands belong to the dimer with two C-H...O hydrogen bonds. This observation includes the HCOF dimer to the class of hydrogen bonded complexes showing blue shift in their vibrational energies.     

Preparation, solid-state characterization, and computational study of a crown ether attached to a squaramide

[structure: see text] Crystals of a disecondary squaramide covalently linked to a crown ether presents a great variety of inter- and intramolecular nonbonded interactions including C-H/pi contacts, C-H...O and N-H...O hydrogen bonds, and pi-pi stacking between squaramide rings. Latter interaction, the stacking between squaramide rings, can be considered as an experimental evidence for the proposed aromaticity of squaramide when it is forming hydrogen bonds, either as acceptor or donor.     

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.     

CH...O and CH...F links form the cage structure of dioxane-trifluoromethane

The molecular beam Fourier transform microwave spectrum of 1,4-dioxane-trifluoromethane has been assigned and measured. The two subunits form a cage stabilized by one C-H...O and two C-H...F weak hydrogen bonds. The C-H...O link involves the axial lone pair of one of the two equivalent ring oxygens, while the two C-H...F bridges connect trifluoromethane to the two axial hydrogens in positions 3 and 5. The dissociation energy has been estimated from the D(J) centrifugal distortion parameter to be approximately 6.8 kJ/mol.