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An intermolecular force (IMF) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules. Both sets of forces are essential parts of force fields frequently used in molecular mechanics.
Physisorption, also called physical adsorption, is a process in which the electronic structure of the atom or molecule is barely perturbed upon adsorption.
The van der Waals radius, rw, of an atom is the radius of an imaginary hard sphere representing the distance of closest approach for another atom. It is named after Johannes Diderik van der Waals, winner of the 1910 Nobel Prize in Physics, as he was the first to recognise that atoms were not simply points and to demonstrate the physical consequences of their size through the van der Waals equation of state.
In molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and therefore more susceptible to disturbance. The van der Waals force quickly vanishes at longer distances between interacting molecules.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Adhesion is the tendency of dissimilar particles or surfaces to cling to one another.
The DLVO theory explains the aggregation and kinetic stability of aqueous dispersions quantitatively and describes the force between charged surfaces interacting through a liquid medium. It combines the effects of the van der Waals attraction and the electrostatic repulsion due to the so-called double layer of counterions. The electrostatic part of the DLVO interaction is computed in the mean field approximation in the limit of low surface potentials - that is when the potential energy of an elementary charge on the surface is much smaller than the thermal energy scale, . For two spheres of radius each having a charge separated by a center-to-center distance in a fluid of dielectric constant containing a concentration of monovalent ions, the electrostatic potential takes the form of a screened-Coulomb or Yukawa potential,
Cyclohexane conformations are any of several three-dimensional shapes adopted by molecules of cyclohexane. Because many compounds feature structurally similar six-membered rings, the structure and dynamics of cyclohexane are important prototypes of a wide range of compounds.
In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds. While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers. Conformations that correspond to local maxima on the energy surface are the transition states between the local-minimum conformational isomers. Rotations about single bonds involve overcoming a rotational energy barrier to interconvert one conformer to another. If the energy barrier is low, there is free rotation and a sample of the compound exists as a rapidly equilibrating mixture of multiple conformers; if the energy barrier is high enough then there is restricted rotation, a molecule may exist for a relatively long time period as a stable rotational isomer or rotamer. When the time scale for interconversion is long enough for isolation of individual rotamers, the isomers are termed atropisomers. The ring-flip of substituted cyclohexanes constitutes another common form of conformational isomerism.
In chemistry, a molecule experiences strain when its chemical structure undergoes some stress which raises its internal energy in comparison to a strain-free reference compound. The internal energy of a molecule consists of all the energy stored within it. A strained molecule has an additional amount of internal energy which an unstrained molecule does not. This extra internal energy, or strain energy, can be likened to a compressed spring. Much like a compressed spring must be held in place to prevent release of its potential energy, a molecule can be held in an energetically unfavorable conformation by the bonds within that molecule. Without the bonds holding the conformation in place, the strain energy would be released.
In organic chemistry, ring strain is a type of instability that exists when bonds in a molecule form angles that are abnormal. Strain is most commonly discussed for small rings such as cyclopropanes and cyclobutanes, whose internal angles are substantially smaller than the idealized value of approximately 109°. Because of their high strain, the heat of combustion for these small rings is elevated.
In chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The chemical energy released in the formation of non-covalent interactions is typically on the order of 1–5 kcal/mol. Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, and hydrophobic effects.
In organic chemistry, hyperconjugation refers to the delocalization of electrons with the participation of bonds of primarily σ-character. Usually, hyperconjugation involves the interaction of the electrons in a sigma (σ) orbital with an adjacent unpopulated non-bonding p or antibonding σ* or π* orbitals to give a pair of extended molecular orbitals. However, sometimes, low-lying antibonding σ* orbitals may also interact with filled orbitals of lone pair character (n) in what is termed negative hyperconjugation. Increased electron delocalization associated with hyperconjugation increases the stability of the system. In particular, the new orbital with bonding character is stabilized, resulting in an overall stabilization of the molecule. Only electrons in bonds that are in the β position can have this sort of direct stabilizing effect — donating from a sigma bond on an atom to an orbital in another atom directly attached to it. However, extended versions of hyperconjugation can be important as well. The Baker–Nathan effect, sometimes used synonymously for hyperconjugation, is a specific application of it to certain chemical reactions or types of structures.
In chemistry, pi stacking refers to the presumptive attractive, noncovalent pi interactions between the pi bonds of aromatic rings. However this is a misleading description of the phenomena since direct stacking of aromatic rings is electrostatically repulsive. What is more commonly observed is either a staggered stacking or pi-teeing interaction both of which are electrostatic attractive For example, the most commonly observed interactions between aromatic rings of amino acid residues in proteins is a staggered stacked followed by a perpendicular orientation. Sandwiched orientations are relatively rare.
In organic chemistry, the anomeric effect or Edward-Lemieux effect is a stereoelectronic effect that describes the tendency of heteroatomic substituents adjacent to a heteroatom within a cyclohexane ring to prefer the axial orientation instead of the less hindered equatorial orientation that would be expected from steric considerations. This effect was originally observed in pyranose rings by J. T. Edward in 1955 when studying carbohydrate chemistry.
Allylic strain in organic chemistry is a type of strain energy resulting from the interaction between a substituent on one end of an olefin with an allylic substituent on the other end. If the substituents are large enough in size, they can sterically interfere with each other such that one conformer is greatly favored over the other. Allylic strain was first recognized in the literature in 1965 by Johnson and Malhotra. The authors were investigating cyclohexane conformations including endocyclic and exocylic double bonds when they noticed certain conformations were disfavored due to the geometry constraints caused by the double bond. Organic chemists capitalize on the rigidity resulting from allylic strain for use in asymmetric reactions.
A-values are numerical values used in the determination of the most stable orientation of atoms in a molecule, as well as a general representation of steric bulk. A-values are derived from energy measurements of the different cyclohexane conformations of a monosubstituted cyclohexane chemical. Substituents on a cyclohexane ring prefer to reside in the equatorial position to the axial. The difference in Gibbs free energy (ΔG) between the higher energy conformation and the lower energy conformation is the A-value for that particular substituent.
Gas is one of the four fundamental states of matter. The others are solid, liquid, and plasma.
Membrane fusion is a key biophysical process that is essential for the functioning of life itself. It is defined as the event where two lipid bilayers approach each other and then merge to form a single continuous structure. In living beings, cells are made of an outer coat made of lipid bilayers; which then cause fusion to take place in events such as fertilization, embryogenesis and even infections by various types of bacteria and viruses. It is therefore an extremely important event to study. From an evolutionary angle, fusion is an extremely controlled phenomenon. Random fusion can result in severe problems to the normal functioning of the human body. Fusion of biological membranes is mediated by proteins. Regardless of the complexity of the system, fusion essentially occurs due to the interplay of various interfacial forces, namely hydration repulsion, hydrophobic attraction and van der Waals forces.
Dispersion stabilized molecules are molecules where the London dispersion force (LDF), a non-covalent attractive force between atoms and molecules, plays a significant role in promoting the molecule's stability. Distinct from steric hindrance, dispersion stabilization has only recently been considered in depth by organic and inorganic chemists after earlier gaining prominence in protein science and supramolecular chemistry. Although usually weaker than covalent bonding and other forms of non-covalent interactions like hydrogen bonding, dispersion forces are known to be a significant if not dominating stabilizing force in certain organic, inorganic, and main group molecules, stabilizing otherwise reactive moieties and exotic bonding.
References
- ↑ Organic chemistry 4th. Ed., Morrison and Boyd ISBN 0-205-05838-8
- ↑ Rzepa, Henry S.; Cass, M.E.; Hii, K.K. "Mechanisms that Interchange Axial and Equatorial Atoms in Fluxional processes" . Retrieved 2008-03-27.
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