Molecular symmetryIn chemistry, molecular symmetry 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 whether or not it has a dipole moment, as well as its allowed spectroscopic transitions. To do this it is necessary to use group theory. This involves classifying the states of the molecule using the irreducible representations from the character table of the symmetry group of the molecule.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Conformational isomerismIn chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). 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.
GadoliniumGadolinium is a chemical element with the symbol Gd and atomic number 64. Gadolinium is a silvery-white metal when oxidation is removed. It is only slightly malleable and is a ductile rare-earth element. Gadolinium reacts with atmospheric oxygen or moisture slowly to form a black coating. Gadolinium below its Curie point of is ferromagnetic, with an attraction to a magnetic field higher than that of nickel. Above this temperature it is the most paramagnetic element. It is found in nature only in an oxidized form.
Metal ions in aqueous solutionA metal ion in aqueous solution or aqua ion is a cation, dissolved in water, of chemical formula [M(H2O)n]z+. The solvation number, n, determined by a variety of experimental methods is 4 for Li+ and Be2+ and 6 for most elements in periods 3 and 4 of the periodic table. Lanthanide and actinide aqua ions have higher solvation numbers (often 8 to 9), with the highest known being 11 for Ac3+. The strength of the bonds between the metal ion and water molecules in the primary solvation shell increases with the electrical charge, z, on the metal ion and decreases as its ionic radius, r, increases.
Tricapped trigonal prismatic molecular geometryIn chemistry, the tricapped trigonal prismatic molecular geometry describes the shape of compounds where nine atoms, groups of atoms, or ligands are arranged around a central atom, defining the vertices of a triaugmented triangular prism (a trigonal prism with an extra atom attached to each of its three rectangular faces). It is very similar to the capped square antiprismatic molecular geometry, and there is some dispute over the specific geometry exhibited by certain molecules.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
SymmetrySymmetry () in everyday language refers to a sense of harmonious and beautiful proportion and balance. In mathematics, the term has a more precise definition and is usually used to refer to an object that is invariant under some transformations, such as translation, reflection, rotation, or scaling. Although these two meanings of the word can sometimes be told apart, they are intricately related, and hence are discussed together in this article.
Dihedral angleA dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimensions, a dihedral angle represents the angle between two hyperplanes.
Stability constants of complexesIn coordination chemistry, a stability constant (also called formation constant or binding constant) is an equilibrium constant for the formation of a complex in solution. It is a measure of the strength of the interaction between the reagents that come together to form the complex. There are two main kinds of complex: compounds formed by the interaction of a metal ion with a ligand and supramolecular complexes, such as host–guest complexes and complexes of anions.
Model categoryIn mathematics, particularly in homotopy theory, a model category is a with distinguished classes of morphisms ('arrows') called 'weak equivalences', 'fibrations' and 'cofibrations' satisfying certain axioms relating them. These abstract from the category of topological spaces or of chain complexes ( theory). The concept was introduced by . In recent decades, the language of model categories has been used in some parts of algebraic K-theory and algebraic geometry, where homotopy-theoretic approaches led to deep results.
Symmetry groupIn group theory, the symmetry group of a geometric object is the group of all transformations under which the object is invariant, endowed with the group operation of composition. Such a transformation is an invertible mapping of the ambient space which takes the object to itself, and which preserves all the relevant structure of the object. A frequent notation for the symmetry group of an object X is G = Sym(X). For an object in a metric space, its symmetries form a subgroup of the isometry group of the ambient space.
Symmetry in mathematicsSymmetry occurs not only in geometry, but also in other branches of mathematics. Symmetry is a type of invariance: the property that a mathematical object remains unchanged under a set of operations or transformations. Given a structured object X of any sort, a symmetry is a mapping of the object onto itself which preserves the structure. This can occur in many ways; for example, if X is a set with no additional structure, a symmetry is a bijective map from the set to itself, giving rise to permutation groups.
Weak equivalence (homotopy theory)In mathematics, a weak equivalence is a notion from homotopy theory that in some sense identifies objects that have the same "shape". This notion is formalized in the axiomatic definition of a . A model category is a with classes of morphisms called weak equivalences, fibrations, and cofibrations, satisfying several axioms. The associated of a model category has the same objects, but the morphisms are changed in order to make the weak equivalences into isomorphisms.
Folding funnelThe folding funnel hypothesis is a specific version of the energy landscape theory of protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells. Although energy landscapes may be "rough", with many non-native local minima in which partially folded proteins can become trapped, the folding funnel hypothesis assumes that the native state is a deep free energy minimum with steep walls, corresponding to a single well-defined tertiary structure.
Homological algebraHomological algebra is the branch of mathematics that studies homology in a general algebraic setting. It is a relatively young discipline, whose origins can be traced to investigations in combinatorial topology (a precursor to algebraic topology) and abstract algebra (theory of modules and syzygies) at the end of the 19th century, chiefly by Henri Poincaré and David Hilbert. Homological algebra is the study of homological functors and the intricate algebraic structures that they entail; its development was closely intertwined with the emergence of .
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
Coordination sphereIn coordination chemistry, the first coordination sphere refers to the array of molecules and ions (the ligands) directly attached to the central metal atom. The second coordination sphere consists of molecules and ions that attached in various ways to the first coordination sphere. The first coordination sphere refers to the molecules that are attached directly to the metal. The interactions between the first and second coordination spheres usually involve hydrogen-bonding. For charged complexes, ion pairing is important.
Icosahedral symmetryIn mathematics, and especially in geometry, an object has icosahedral symmetry if it has the same symmetries as a regular icosahedron. Examples of other polyhedra with icosahedral symmetry include the regular dodecahedron (the dual of the icosahedron) and the rhombic triacontahedron. Every polyhedron with icosahedral symmetry has 60 rotational (or orientation-preserving) symmetries and 60 orientation-reversing symmetries (that combine a rotation and a reflection), for a total symmetry order of 120.
A valueA-values are numerical values used in the determination of the most stable orientation of atoms in a molecule (conformational analysis), 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.
