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Molecular binding is an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other. It is formed when atoms or molecules bind together by sharing of electrons. It often, but not always, involves some chemical bonding.
On the molecular level, the interlocked molecules cannot be separated without the breaking of the covalent bonds that comprise the conjoined molecules; this is referred to as a mechanical bond. Examples of mechanically interlocked molecular architectures include catenanes , rotaxanes , molecular knots , and molecular Borromean rings .
A major application of Walsh diagrams is to explain the regularity in structure observed for related molecules having identical numbers of valence electrons (e.g. why H 2 O and H 2 S look similar), and to account for how molecules alter their geometries as their number of electrons or spin state changes.
The states - often termed tense (T) and relaxed (R) - differ in affinity for the ligand molecule. The ratio between the two states is regulated by the binding of ligand molecules that stabilizes the higher-affinity state. Importantly, all subunits of a molecule change states at the same time, a phenomenon known as "concerted transition".
Bond order is the number of chemical bonds between a pair of atoms. The bond order of a molecule can be calculated by subtracting the number of electrons in anti-bonding orbitals from the number of bonding orbitals, and the resulting number is then divided by two. A molecule is expected to be stable if it has bond order larger than zero.
The design of a molecular dynamics simulation should account for the available computational power. Simulation size (n = number of particles), timestep, and total time duration must be selected so that the calculation can finish within a reasonable time period. However, the simulations should be long enough to be relevant to the time scales of ...
Water, for example, is strongly cohesive as each molecule may make four hydrogen bonds to other water molecules in a tetrahedral configuration. This results in a relatively strong Coulomb force between molecules. In simple terms, the polarity (a state in which a molecule is oppositely charged on its poles) of water molecules allows them to be ...
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.