Conventional H-bond

Their enthalpies of formation are substantial, 13-30kJmol, and lie in the range for conventional H bonds. Some examples are listed below. 

In fact, as noticed by Hobza and Havlas [105], the published definitions of the H- bond are not unambiguous and many exist . Nowadays, the concept of a hydrogen bond is much broader than it was expected nearly a century ago [80,82], and that is why it permits, together with the conventional H-bonds, an existence of a wide class of those, say nonconventional ones, identified during the last three decades experimentally and theoretically, which do not partially... 

Protein chemistry provides again an illustrative example of the new light cast on conventional H-bonds. Baker and coworkers [32, 33] have used the geometric characteristics of H-bonds in a dataset of 698 high-resolution protein crystal structures to develop an orientation-dependent hydrogen bonding potential. Upon analyzing more than 100,000 H-bonds (most of them N-H- - -O backbone-backbone links), these authors concluded that quantum effects are utterly essential to explain the spatial orientation of these H-bonds [32] and even stated explicitly their partial covalent nature [33]. 

The stabilizing role of C-H- O = C contacts in base pairs was evaluated for the Watson Crick adenine-uracil (AU) pair by Starikov and Steiner [125]. Their ab initio calculations indicated these bonds contributed only about 6% to the total interaction energy. A better estimate might be achieved via the correlated calculations of the dimer of pyrimidine [126] (related to DNA base pairs) like that shown in Fig. 3. This dimer does not contain any conventional H-bonds,... 

A wide assortment of different possible geometries for the uracil dimer were examined [127] in 1998. The most stable of all these contained a pair of NH- -O bonds, but another was identified, only slightly less stable than the others, in which one of these conventional H-bonds was replaced by CH- -O = C. There was no way of estimating the energetic contribution of this particular interaction, as it was secondary to the stronger NH- -O bond. A study of the adenine thymine pair [128] noted a blue shift of the C-H stretching frequency, an indication of a H-bond, but the authors did not attempt to extract an interaction energy. 

As in the case of the nucleic acids, systems that model various segments of proteins tend to vary in both size and relevance to the full systems. One is beset with the same problems that the CH- X bonds of interest are typically secondary to stronger conventional H-bonds, and consequently distorted. 

Stronger conventional H-bond. These CH- -O interactions are explicitly designated by broken lines in Fig. 8, ignoring the conventional bonds which are also present. Unfortunately, the authors focused on vibrational frequencies, ignoring the energetics of the various structures. 

Alanine was reinvestigated later, again pairing it with a molecule of water [143]. Quite a number of minima identified on that surface contained a CH- -O interaction, but unlike the earlier work which isolated the CH- - -O bond as the only H-bond present, these interactions were combined with a stronger conventional H-bond. This combination prevented an assessment of the energetic contribution of either one separate from the other. On the positive side, this work demonstrated that it was possible to submerge such systems in model solvents/proteins, and obtain meaningful results. 

A -methyl maleimide that would not be present in the His residue.) In this case, as there were no conventional H-bonds present, one could at least in principle, consider the H-bond energy of each as roughly half the total interaction energy, which would lead to an estimate of 1.4-1.7 kcal/mol for each. On the other hand, the two CH- -0 bonds are clearly angularly distorted so the numerical value is apt to represent an underestimate. 

The interaction between proteins and nucleic acids has been considered as well. Dabkowska et al. [159] began with the most stable tautomers of Gly and uracil, identifying 23 different minima on the surfaee that eharaeterized their pairing. While most of these configurations, particularly the most stable, contained only conventional H-bonds, several minima did appear to contain either CH- -O or CH N, but no attempt was made to determine the energetic contribution of any individual bonds. These interactions were the subject of another set of calculations [160] which paired a model of the protein backbone with nucleic acids. Some of the minima contained secondary CH- - -O bonds, along with the more standard H-bonds. 

Note With only few exceptions, chloroform forms complexes with conventional H-bonds more than 75 of them are collected in Ref [43]. The complex BrsC-H OH2 also refers to that with conventional H-bond [46b]. A red shift of the V (C-H) stretch is experimentally observed for the CClsH-water complex [81,91]. See also Ref [lOOp] for the blue-shifting complex BrsC H - (0H2)2... 

Bi U A2—H2 M belongs to a subclass of blue-shifted H-bonded systems while interacting with another molecule M e B2 U Ai—Hi and forming one conventional H-bond Ai-Hi Bi and at least one nonconventional A2-H2 B2. Let us explain this suggestion in more details invoking the H2CO as an example (see Refs. [76d-f]). 

In contrast to the view enunciated above, that red and blue-shifting systems are fundamentally rather similar, an alternative interpretation had been evolving, particularly amongst a group of researchers in Prague. A series of papers [204-209] opined that there is a physically important difference as follows. In either sort of H-bond, there is a certain amount of electron density that is transferred from the proton acceptor molecule to the donor. In conventional H-bonds of the OH- - -O variety, the bulk of this density appears in... 

A novel type of supramolecular hydrogen-bonded liquid-crystalline materials that are conceptually different from conventional H-bonded systems such... 

In a next stq> C-H...O and C-H...7I interactions could be taken into account. It has already been found that backbone-backbone C2 -H...04 interactions in DNA and RNA and C5 -H...02 interactions in die RNA backbone do frequently occur. If these interactions are considered in addition to the conventional H-bonds, the size of nucleotide clusters is likely to increase further. 

Blue-shifted. - Cubero et used AIM to examine the nature of what they termed the anti-hydrogen bond interaction . Upon formation of the anti H-bond the X-H bond shortens and its vibrational frequency blue-shifts contrary to a H-bond. Amongst others the topological properties of p have been determined for a series of C-H... n complexes, which exhibit either anti H-bond or normal H-bond character. According to a set of topological criteria utilized to characterize conventional H-bonds no relevant difference was found in the two classes of C-H... 71 complexes. Since the anti H-bonds are just a special type of H-bond the qualifier anti is misleading and was abandoned in later work. 

---