In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 of one alpha-amino acid and N2 of another, along a peptide or protein chain.
A random coil is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules. The conformation's name is derived from the idea that, in the absence of specific, stabilizing interactions, a polymer backbone will "sample" all possible conformations randomly. Many linear, unbranched homopolymers — in solution, or above their melting temperatures — assume (approximate) random coils.
In chemistry, a lone pair refers to a pair of valence electrons that are not shared with another atom in a covalent bond and is sometimes called an unshared pair or non-bonding pair. Lone pairs are found in the outermost electron shell of atoms. They can be identified by using a Lewis structure. Electron pairs are therefore considered lone pairs if two electrons are paired but are not used in chemical bonding. Thus, the number of lone pair electrons plus the number of bonding electrons equals the total number of valence electrons around an atom.
Rotational symmetry, also known as radial symmetry in geometry, is the property a shape has when it looks the same after some rotation by a partial turn. An object's degree of rotational symmetry is the number of distinct orientations in which it looks exactly the same for each rotation.
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom.
Cyclopentane (also called C pentane) is a highly flammable alicyclic hydrocarbon with chemical formula C5H10 and CAS number 287-92-3, consisting of a ring of five carbon atoms each bonded with two hydrogen atoms above and below the plane. It occurs as a colorless liquid with a petrol-like odor. Its melting point is −94 °C and its boiling point is 49 °C. Cyclopentane is in the class of cycloalkanes, being alkanes that have one or more rings of carbon atoms. It is formed by cracking cyclohexane in the presence of alumina at a high temperature and pressure.
In organic chemistry, 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.
Alkane stereochemistry concerns the stereochemistry of alkanes. Alkane conformers are one of the subjects of alkane stereochemistry.
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 geometry, a point group in three dimensions is an isometry group in three dimensions that leaves the origin fixed, or correspondingly, an isometry group of a sphere. It is a subgroup of the orthogonal group O(3), the group of all isometries that leave the origin fixed, or correspondingly, the group of orthogonal matrices. O(3) itself is a subgroup of the Euclidean group E(3) of all isometries.
In geometry, dihedral symmetry in three dimensions is one of three infinite sequences of point groups in three dimensions which have a symmetry group that as an abstract group is a dihedral group Dihn.
In geometry, a two-dimensional point group or rosette group is a group of geometric symmetries (isometries) that keep at least one point fixed in a plane. Every such group is a subgroup of the orthogonal group O(2), including O(2) itself. Its elements are rotations and reflections, and every such group containing only rotations is a subgroup of the special orthogonal group SO(2), including SO(2) itself. That group is isomorphic to R/Z and the first unitary group, U(1), a group also known as the circle group.
In organic chemistry, a ring flip is the interconversion of cyclic conformers that have equivalent ring shapes that results in the exchange of nonequivalent substituent positions. The overall process generally takes place over several steps, involving coupled rotations about several of the molecule's single bonds, in conjunction with minor deformations of bond angles. Most commonly, the term is used to refer to the interconversion of the two chair conformers of cyclohexane derivatives, which is specifically referred to as a chair flip, although other cycloalkanes and inorganic rings undergo similar processes.
Pyranose is a collective term for saccharides that have a chemical structure that includes a six-membered ring consisting of five carbon atoms and one oxygen atom. There may be other carbons external to the ring. The name derives from its similarity to the oxygen heterocycle pyran, but the pyranose ring does not have double bonds. A pyranose in which the anomeric OH at C(l) has been converted into an OR group is called a pyranoside.
A molecular model, is a physical model that represents molecules and their processes. The creation of mathematical models of molecular properties and behaviour is molecular modelling, and their graphical depiction is molecular graphics, but these topics are closely linked and each uses techniques from the others. In this article, "molecular model" will primarily refer to systems containing more than one atom and where nuclear structure is neglected. The electronic structure is often also omitted or represented in a highly sophisticated way.
In chemistry, the Z-matrix is a way to represent a system built of atoms. A Z-matrix is also known as an internal coordinate representation. It provides a description of each atom in a molecule in terms of its atomic number, bond length, bond angle, and dihedral angle, the so-called internal coordinates, although it is not always the case that a Z-matrix will give information regarding bonding since the matrix itself is based on a series of vectors describing atomic orientations in space. However, it is convenient to write a Z-matrix in terms of bond lengths, angles, and dihedrals since this will preserve the actual bonding characteristics. The name arises because the Z-matrix assigns the second atom along the Z axis from the first atom, which is at the origin.
Molecular symmetry in chemistry describes the symmetry present in molecules and the classification of these molecules according to their symmetry. Molecular symmetry is a fundamental concept in chemistry, as it can be used to predict or explain many of a molecule's chemical properties, such as its dipole moment and its allowed spectroscopic transitions. To do this it is necessary to classify the states of the molecule using the irreducible representations from the character table of the symmetry group of the molecule. Many university level textbooks on physical chemistry, quantum chemistry, spectroscopy and inorganic chemistry devote a chapter to symmetry.
In chemistry, isomers are molecules or polyatomic ions with identical molecular formulas — that is, same number of atoms of each element — but distinct arrangements of atoms in space. Isomerism is existence or possibility of isomers.
Carbohydrate conformation refers to the overall three-dimensional structure adopted by a carbohydrate (saccharide) molecule as a result of the through-bond and through-space physical forces it experiences arising from its molecular structure. The physical forces that dictate the three-dimensional shapes of all molecules—here, of all monosaccharide, oligosaccharide, and polysaccharide molecules—are sometimes summarily captured by such terms as "steric interactions" and "stereoelectronic effects".
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