Hydrogen bond chemical reactivity

A special type of substituent effect which has proved veiy valuable in the study of reaction mechanisms is the replacement of an atom by one of its isotopes. Isotopic substitution most often involves replacing protium by deuterium (or tritium) but is applicable to nuclei other than hydrogen. The quantitative differences are largest, however, for hydrogen, because its isotopes have the largest relative mass differences. Isotopic substitution usually has no effect on the qualitative chemical reactivity of the substrate, but often has an easily measured effect on the rate at which reaction occurs. Let us consider how this modification of the rate arises. Initially, the discussion will concern primary kinetic isotope effects, those in which a bond to the isotopically substituted atom is broken in the rate-determining step. We will use C—H bonds as the specific topic of discussion, but the same concepts apply for other elements. 

Many biological processes involve an "association" between two species in a step prior to some subsequent transformation. This association can take many forms. It can be a weak association of the attractive van der Waals type, or a stronger interaction such as a hydrogen bond. It can be an electrostatic attraction between a positively charged atom of one molecule and a negatively charged atom of another. Covalent bond formation between two species of complementary chemical reactivity represents an extreme kind of association. It often occurs in biological processes in which aldehydes or ketones react with amines via imine intermediates. 

The rate of reaction of a series of nucleophiles with a single substrate is related to the basicity when the nucleophilic atom is the same and the nucleophiles are closely related in chemical type. Thus, although the rates parallel the basicities of anilines (Tables VII and VIII) as a class and of pyridine bases (Tables VII and VIII) as a class, the less basic anilines are much more reactive. This difference in reactivity is based on a lower energy of activation as is the reactivity sequence piperidine > ammonia > aniline. Further relationships among the nucleophiles found in this work are morpholine vs. piperidine (Table III) methoxide vs. 4-nitrophenoxide (Table II) and alkoxides vs. piperidine (Tables II, III, and VIII). Hydrogen bonding in the transition state and acid catalysis increase the rates of reaction of anilines. Reaction rates of the pyridine bases are decreased by steric hindrance between their alpha hydrogens and the substituents or... 

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

The reactivity of protons in chemical and biological systems is modified if the proton is held within an intramolecular hydrogen bond. In this section, the... 

The usefulness of potential energy hypersurfaces in describing reaction dynamics and chemical reactivity is well illustrated by Levine and Bernstein [84] and Shaik et al. [85] books. See also the fundamental paper of Hase [86]. This success does not assure that the coordinate representation of quantum system is necessarily truthful. It goes without saying, the coordinate representation is an extremely useful mathematical model. However, from recent inelastic neutron scattering experiments on hydrogen bonded system, the idea that the BO approximation may be inadequate has been advanced by Kearley and coworkers[87]. 

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