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In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. The simplest case is a pair of water molecules with one hydrogen bond between them, which is called the water dimer and is often used as a model system. When more molecules are present, as is the case with liquid water, more bonds are possible because the oxygen of ...
Even for small molecules like carbohydrates, the recognition process can not be predicted or designed even assuming that each individual hydrogen bond's strength is exactly known. [26] However, as Mobley et al. [ 27 ] concluded, the accurate prediction of the molecular recognition events needs to go beyond the static snapshot of a single frame ...
Molecular self-assembly is a key concept in supramolecular chemistry. [6] [7] [8] This is because assembly of molecules in such systems is directed through non-covalent interactions (e.g., hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-stacking interactions, and/or electrostatic) as well as electromagnetic interactions.
The first theoretical study of the water dimer was an ab initio calculation published in 1968 by Morokuma and Pedersen. [10] Since then, the water dimer has been the focus of sustained interest by theoretical chemists concerned with hydrogen bonding—a search of the CAS database up to 2006 returns over 1100 related references (73 of them in 2005).
Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes. Hydrogen bonding is the chemical mechanism that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form ...
The theory is also applied to so-called hydrogen–hydrogen bond s [5] as they occur in molecules such as phenanthrene and chrysene. In these compounds, the distance between two ortho hydrogen atoms again is shorter than their van der Waals radii, and according to in silico experiments based on this theory, a bond path is identified between them.
Isovalent hybridization is used to explain bond angles of those molecules that is inconsistent with the generalized simple sp, sp 2 and sp 3 hybridization. For molecules containing lone pairs, the true hybridization of these molecules depends on the amount of s and p characters of the central atom which is related to its electronegativity.
This bonding scheme is succinctly summarized by the following two resonance structures: I—I···I − ↔ I − ···I—I (where "—" represents a single bond and "···" represents a "dummy bond" with formal bond order 0 whose purpose is only to indicate connectivity), which when averaged reproduces the I—I bond order of 0.5 obtained ...
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