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An ubiquitous example of a hydrogen bond is found between water molecules. 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 ...
A molecular vibration is a periodic motion of the atoms of a molecule relative to each other, such that the center of mass of the molecule remains unchanged. The typical vibrational frequencies range from less than 10 13 Hz to approximately 10 14 Hz, corresponding to wavenumbers of approximately 300 to 3000 cm −1 and wavelengths of approximately 30 to 3 μm.
MO diagram of dihydrogen Bond breaking in MO diagram. The smallest molecule, hydrogen gas exists as dihydrogen (H-H) with a single covalent bond between two hydrogen atoms. As each hydrogen atom has a single 1s atomic orbital for its electron, the bond forms by overlap of these two atomic orbitals. In the figure the two atomic orbitals are ...
Model of hydrogen bonds (1) between molecules of water. A single water molecule can participate in a maximum of four hydrogen bonds because it can accept two bonds using the lone pairs on oxygen and donate two hydrogen atoms. Other molecules like hydrogen fluoride, ammonia, and methanol can also form hydrogen bonds.
In some important cases (topological index calculation etc.) the following classical definition is sufficient: a molecular graph is a connected, undirected graph which admits a one-to-one correspondence with the structural formula of a chemical compound in which the vertices of the graph correspond to atoms of the molecule and edges of the ...
In accordance with the VSEPR (valence-shell electron pair repulsion theory), the bond angles between the electron bonds are arccos(− 1 / 3 ) = 109.47°. For example, methane (CH 4) is a tetrahedral molecule. Octahedral: Octa-signifies eight, and -hedral relates to a face of a solid, so "octahedral" means "having eight faces". The bond ...
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Secondary structure is defined by hydrogen bonding, so the exact definition of a hydrogen bond is critical. The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ±q 1 ≈ 0.42e to the carbonyl carbon and oxygen, respectively, and charges of ±q 2 ≈ 0.20e to ...