Hydrogen Bonded Dimers

Cyclic dimers of carboxylic acids represent important model systems forming two coupled intermolecular hydrogen bonds [Fig. 15.1 (d), inset of Fig. 15.4]. The linear vibrational spectra of carboxylic acid dimers have been studied in detail, both in the gas and the liquid phase, and a substantial theoretical effort has been undertaken to understand the line shape of their 0-H and/or O-D stretching bands. In contrast, there have been only a few experiments on the nonlinear vibrational 

Dimer structures containing two O-H - -O (OH/OH dimer) or two O-D- -O (OD/OD dimer) hydrogen bonds were dissolved in CCI4 at concentrations between 0.2 and 0.8 M. Two-color pump-probe experiments with independently tunable pump and probe pulses were performed with a 100 fs time resolution. Approximately 1% of the dimers present in the sample volume were excited by the 1 pj pump pulse. After interaction with the sample, the probe pulses were spectrally dispersed to measure transient vibrational spectra with a spectral resolution of 6 cm 1. 

The time evolution of the nonlinear O-H stretching absorption shows pronounced oscillatory signals for all types of dimers studied. In Fig. 15.5, data for OD/OD dimers are presented which were recorded at 3 different spectral positions in the O-D stretching band. For positive delay times, one finds rate-like kinetics which is due to population and thermal relaxation of the excited dimers and, more importantly, superimposed by very strong oscillatory absorption changes. In contrast to the intramolecular hydrogen bonds discussed above, the time-dependent amplitude of the oscillations displays a slow modulation with an increase and a decrease on a time scale of several hundreds of femtoseconds. 

Such features of a beatnote demonstrate the presence of more than one oscillation frequency. In Fig. 15.6 (a), the Fourier transforms of the oscillatory signals are plotted for the 3 spectral positions. There are 3 prominent frequency components, a strong doublet with maxima at 145 and 170 cm i and a much weaker component around 50 cm h Comparative pump-probe studies of OH/OH dimers reveal a similar doublet at 145 and 170 cm i with slightly changed relative intensities of the two components. The 50 cm i component is practically absent in the OH/OH 

O-D stretching oscillator and oscillatory contributions. Dash-dotted lines Numerical fits ofthe rate-like signals, (d) - (f) Oscillatory signals after subtraction ofthe rate-like components. The oscillations are due to coherent wavepacket motions along several low-frequency modes. 

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Figure 9.46 shows an example of a fluorescence excitation spectmm of hydrogen bonded dimers of x-tetrazine (1,2,4,5-tetraazabenzene). The pressure of x-tetrazine seeded into helium carrier gas at 4 atm pressure was about 0.001 atm. Expansion was through a 100 pm diameter nozzle. A high-resolution (0.005 cm ) dye laser crossed the supersonic jet 5 mm downstream from the nozzle. 

The three bands in Figure 9.46 show resolved rotational stmcture and a rotational temperature of about 1 K. Computer simulation has shown that they are all Ojj bands of dimers. The bottom spectmm is the Ojj band of the planar, doubly hydrogen bonded dimer illustrated. The electronic transition moment is polarized perpendicular to the ring in the — Ag, n — n transition of the monomer and the rotational stmcture of the bottom spectmm is consistent only with it being perpendicular to the molecular plane in the dimer also, as expected. 

Fig. 8. Rephcation. The amino adenosine X and the pentafluorophenyl ester Y form a hydrogen-bonded dimer XY, prior to reaction between the amine and the activated ester groups (shown in the circle). The reaction product is a <7 -amide conformer cis-Z that isomeri2es to the more stable trans- acnide Z. The rephcative process is cataly2ed by the reaction product Z (also referred to as the template). First, a termolecular complex XYZ is formed from X, Y, and Z.

The amide formation reaction (highlighted by the circle) leads to the production of a hydrogen-bonded dimer (ZZ) of the reaction product Z with the template Z. The dimer is in thermodynamic equilibrium with free template in the reaction medium. 

In the vapor phase formic acid forms a hydrogen-bonded dimer ... 

Bond dissociation energies (BDEs) for the oxygen—oxygen and oxygen— hydrogen bonds are 167—184 kj/mol (40.0—44.0 kcal/mol) and 375 kj/mol (89.6 kcal/mol), respectively (10,45). Heats of formation, entropies, andheat capacities of hydroperoxides have been summarized (9). Hydroperoxides exist as hydrogen-bonded dimers in nonpolar solvents and readily form hydrogen-bonded associations with ethers, alcohols, amines, ketones, sulfoxides, and carboxyhc acids (46). Other physical properties of hydroperoxides have been reported (46). 

The structure of lumazine has been studied more precisely by X-ray analysis (72AX(B)659). The crystal structure is built up of almost coplanar, hydrogen-bonded dimers of lumazine with the oxygens of the pyrimidine moiety in the keto form and the observed bond distances indicating the pyrazine ring electrons to be delocalized. 

Imidazoles and pyrazoles with free NH groups form hydrogen-bonded dimers and oligomers (66AHC(6)347). 

In 1951, pyrid-4-thione was concluded from ultraviolet spectral data to exist predominantly as such in ethanolic solution,but no comparisons were made and this conclusion had to be considered as tentative. Pyrid-2-thione has been shown by X-ray crystallography to exist as hydrogen-bonded dimers (201) in the solid state, the posi-... 

The following remarks can be made about Huang s mechanism as on any mechanism involving hydrogen-bonded dimers such as in 19) where the existence of the equilibrium... 

Ueberreiter and Hager19 rather surprisingly found an overall reaction order of 6 at the beginning of ethanediol esterification. They explained this with the existence of hydrogen-bonded dimers. 

Fig. 3. Stereoview of the inclusion complex between a hydrogen-bonded dimer of host 3 with water and methylene chloride as guests. The crystal structure of this compound contains two additional species, a disordered CH Clj and fractional water (donated by S ). Both lie outside the complex between the bound water and an adjacent host unit (taken from Ref.28>)...

The carboxyl functions in the new structures are buried within the clefts in a manner that discourages the formation of the intermolecular hydrogen bonded dimers which are usually observed in the solution and solid phases. Unusual acid-base behavior is one consequence. In the smallest system 11 (represented by the benzene spacer) a tremendous difference in pKa s (6 units) can be observed for the two ionizations 14). 

Unexpectedly, reaction of 73 with 2-aminoimidazole in MeCN in the presence of K2C03 afforded the hydrogen-bonded dimeric product 68, in which the betaine molecule is strongly associated to the corresponding pyridotriazi-nium iodide (Equation 2) <1996T11349>. 

Typical examples are the conversion of the neutral form of an amino acid into its zwitterionic form, the helix-coil transitions in polypeptides and polynucleotides, and other conformational changes in biopolymers. Reactions of higher molecularity in which reactants and products have different dipole moments are subject to the same effect (association of the carboxylic acids to form hydrogen-bonded dimers). Equilibrium involving ions are often more sensitive to the application of an electric field ... 

Broadened band. The Vs (OH) band goes from 30 cm-1 width in the case of gaseous acetic acid monometer, and it increases up to 400 cm-1 for hydrogen-bonded dimers. 

There is also the possibility of Davydov coupling, which is likely to appear when there are double or multiple H-bond systems [7,21-23]. It is responsible for cooperative effects between neighboring hydrogen bonds in cyclic hydrogen bonded dimers, or more generally in hydrogen-bonded chains in solids [ 10,24—34]. 

Philippova and Starodubtzev have also extensively studied the complex-ation behavior of polyacids and PEG, especially, the system of crosslinked of poly(methacrylic acid) and linear poly(ethylene glycol) (Philippova and Starodubtzev, 1995 Philippova et al., 1994). They observed that decreasing the molecular weight of PEG from 6000 to 1500 resulted in its slower diffusion into the swollen network of PMAA, and a drastic decrease in both the stability and equilibrium composition of the intermacromolecular complex. Analysis of dried polymer networks of PMAA with absorbed PEG chains by FT-IR spectroscopy revealed the presence of two types of hydrogen bonded structures (1) dimers of methacrylic acid at absorption frequency of 1700 cm-1 and (2) interpolymer complexes of PMAA and PEG at 1733 cm-1. In addition, they also suggested as a result of their studies, that the hydrogen bonded dimer of PMAA forms preferentially to the intermacromolecular complex between the PMAA network and PEG chains. 

In the course of elaboration of effective new synthetic routes, the compound 63 had been synthesized <1999JHC183>. X-Ray structure analysis provided a final and firm proof of the structure and, thereby, the applicability of the invented method. Rusinov et al. < 1998ZOR290> investigated the structures of the cation of salt 64 and the zwitterionic compound 65 obtained by an addition of triazolopyrimidine derivatives on A -methylpyridinium compounds. The cation 64 was found to form hydrogen-bonded dimers, whereas 65 formed a co-crystal with acetonitrile. 

Figure 22. Structure of the hydrogen-bonded dimer [FeIn2(LHBuH)2]2+. [Adapted from (148b).]...

N. Borho, M. A. Suhm, K. Le Barbu Debus, and A. Zehnacker, Intra vs. intermolecular hydrogen bonding Dimers of alpha hydroxyesters with methanol. Phys. Chem. Chem. Phys. 8, 4449 4460 (2006). 

Further studies by the same authors have demonstrated that PFj acts a hydrogen bond-acceptor template in the assembly of several other interwoven structures. In an extensive study aimed at using a combination of hydrogenbonding motifs to self-assemble pseudorotaxanes into more complex structures it was discovered that PFj assists on the organization of the components that yield the final superstructure [74]. Particularly, it was found that this anion dictates the orientation of the two carboxylic acid groups of the [3]pseudorotaxanes 58 and 59 (see Schemes 27 and 28) when these groups are co-directional with respect to each other the formation of discrete hydrogen-bonded dimers is observed. 

This reduction in crystal symmetry is conveniently illustrated in the systems cinnamide, benzamide, or, in general, any amide RCONH2 packing in a ribbon motif comprising centrosymmetric hydrogen-bonded dimers interlinked by translation (Scheme 16). 

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